data_7BZT # _model_server_result.job_id ESrXtbz2XnZCDdOnkqDjWQ _model_server_result.datetime_utc '2024-10-12 03:18:02' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 7bzt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 7BZT # _exptl.entry_id 7BZT _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 299.492 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPHINGOSINE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 7BZT _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BZT _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? 300-meric 300 'complete icosahedral assembly' 1 ? pentameric 5 'icosahedral asymmetric unit' 2 ? 25-meric 25 'icosahedral pentamer' 3 ? 30-meric 30 'icosahedral 23 hexamer' 4 ? pentameric 5 'icosahedral asymmetric unit, std point frame' 5 ? 300-meric 300 'crystal asymmetric unit, crystal frame' 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 (1-60) A,B,C,D,E,F,G,H,I 2 1 A,B,C,D,E,F,G,H,I 3 (1-5) A,B,C,D,E,F,G,H,I 4 (1,2,6,10,23,24) A,B,C,D,E,F,G,H,I 5 P A,B,C,D,E,F,G,H,I 6 (X0)(1-60) # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] P 'transform to point frame' ? ? 0.507598 0.304449 0.806012 0.31778 0.803381 -0.503582 -0.80085 0.511751 0.311047 -426.83109 -162.6256 -5.32362 X0 'transform to crystal frame' ? ? 1 0 0 0 1 0 0 0 1 0 0 0 1 'point symmetry operation' ? ? 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? 0.491697 -0.304576 0.815762 -0.304872 0.817319 0.488919 -0.815651 -0.489103 0.309017 -0.75944 -0.35971 526.46011 3 'point symmetry operation' ? ? -0.330753 -0.797687 0.504279 -0.79787 0.521736 0.301984 -0.503989 -0.302467 -0.809017 428.4426 256.9741 689.9406 4 'point symmetry operation' ? ? -0.330753 -0.79787 -0.503989 -0.797687 0.521736 -0.302467 0.504279 0.301984 -0.809017 694.46348 416.37484 264.517 5 'point symmetry operation' ? ? 0.491697 -0.304872 -0.815651 -0.304576 0.817319 -0.489103 0.815762 0.488919 0.309017 429.67139 257.55611 -161.88974 6 'point symmetry operation' ? ? 0.28272 -0.819672 -0.498204 -0.819672 -0.476221 0.318358 -0.498204 0.318358 -0.806499 536.67563 521.19696 524.27136 7 'point symmetry operation' ? ? 0.795269 -0.51237 -0.324074 -0.517513 -0.295282 -0.803112 0.315797 0.806403 -0.499987 274.47099 689.59346 99.94567 8 'point symmetry operation' ? ? 0.811571 -0.502484 0.298098 0.490623 0.309087 -0.814711 0.317241 0.80745 0.497376 103.43915 267.2862 -163.80732 9 'point symmetry operation' ? ? 0.309097 -0.803676 0.508492 0.811526 0.501669 0.29959 -0.495868 0.320052 0.807268 259.94031 -162.11055 97.51006 10 'point symmetry operation' ? ? -0.017751 -0.999709 0.01635 0.001719 0.016322 0.999865 -0.999841 0.017776 0.001429 527.69519 -5.18507 522.76607 11 'point symmetry operation' ? ? -0.798032 0.510597 -0.320056 0.510597 0.290843 -0.809136 -0.320056 -0.809136 -0.492811 424.79058 265.34492 691.37365 12 'point symmetry operation' ? ? -0.287003 0.816923 -0.500266 0.822361 0.477948 0.308687 0.491275 -0.322806 -0.808978 256.71629 -161.12534 432.46227 13 'point symmetry operation' ? ? 0.017867 0.999783 0.010692 0.006859 -0.010816 0.999918 0.999817 -0.017792 -0.007051 -6.72989 0.58964 6.3105 14 'point symmetry operation' ? ? -0.304742 0.806471 0.506692 -0.808914 -0.499992 0.309299 0.502783 -0.315614 0.804735 -1.47429 527.00525 1.84561 15 'point symmetry operation' ? ? -0.808995 0.504137 0.302278 -0.497587 -0.313557 -0.808758 -0.312944 -0.804691 0.504518 265.22002 690.63301 425.23792 16 'point symmetry operation' ? ? -0.484688 0.309075 0.81826 0.309075 -0.814622 0.490778 0.81826 0.490778 0.29931 94.83138 266.74952 -160.4787 17 'point symmetry operation' ? ? -0.999963 0.000024 0.008579 0.000024 -0.999985 0.005506 0.008579 0.005506 0.999948 525.86975 525.18297 -3.70173 18 'point symmetry operation' ? ? -0.498684 0.300388 -0.813069 0.300388 -0.820007 -0.487191 -0.813069 -0.487191 0.318692 531.14573 528.44146 522.72252 19 'point symmetry operation' ? ? 0.326398 0.795075 -0.511194 0.795075 -0.523413 -0.306422 -0.511194 -0.306422 -0.802986 103.36809 272.02185 691.29364 20 'point symmetry operation' ? ? 0.335049 0.800444 0.497023 0.800444 -0.520084 0.297996 0.497023 0.297996 -0.814964 -166.28901 110.28734 269.05207 21 'point symmetry operation' ? ? -0.499699 -0.286876 0.817314 0.326602 0.811522 0.484524 -0.802267 0.509053 -0.311822 255.97255 -164.42996 423.86064 22 'point symmetry operation' ? ? -0.824883 -0.482024 -0.29533 -0.482024 0.326815 0.812924 -0.29533 0.812924 -0.501931 686.73865 90.11288 260.12471 23 'point symmetry operation' ? ? -0.017751 0.001719 -0.999841 -0.999709 0.016322 0.017776 0.01635 0.999865 0.001429 532.05878 518.33324 -4.19028 24 'point symmetry operation' ? ? 0.806269 0.495837 -0.322608 -0.51103 0.309133 -0.802051 -0.297958 0.811531 0.502632 5.69526 528.44514 -3.80999 25 'point symmetry operation' ? ? 0.508408 0.317475 0.800456 0.308675 0.800594 -0.513585 -0.803891 0.508192 0.309032 -164.93541 106.47428 260.74003 26 'point symmetry operation' ? ? -0.313321 0.806404 -0.50154 -0.814237 -0.499918 -0.295129 -0.488722 0.315902 0.813238 266.77173 687.83411 95.14071 27 'point symmetry operation' ? ? 0.009172 0.999825 -0.016313 -0.007225 -0.016247 -0.999842 -0.999932 0.009289 0.007075 2.67875 533.25889 523.53579 28 'point symmetry operation' ? ? -0.287003 0.822361 0.491275 0.816923 0.477948 -0.322806 -0.500266 0.308687 -0.808978 -6.27602 6.89334 528.01641 29 'point symmetry operation' ? ? -0.792543 0.519262 0.319754 0.519262 0.299706 0.800339 0.319754 0.800339 -0.507163 252.2826 -163.84323 102.39051 30 'point symmetry operation' ? ? -0.808808 0.5094 -0.293839 -0.488849 -0.304648 0.817445 0.326889 0.804799 0.495422 421.03539 257.00131 -165.14139 31 'point symmetry operation' ? ? -0.009288 -0.999899 -0.010728 -0.001353 0.010741 -0.999941 0.999956 -0.009273 -0.001453 532.65355 524.62793 2.55395 32 'point symmetry operation' ? ? 0.309025 -0.809161 -0.499762 0.811663 0.498266 -0.304851 0.495688 -0.311431 0.810743 527.37227 -1.80416 1.03293 33 'point symmetry operation' ? ? 0.806269 -0.51103 -0.297958 0.495837 0.309133 0.811531 -0.322608 -0.802051 0.502632 264.32398 -163.09185 427.59221 34 'point symmetry operation' ? ? 0.795269 -0.517513 0.315797 -0.51237 -0.295282 0.806403 -0.324074 -0.803112 -0.499987 107.03247 263.65896 692.74137 35 'point symmetry operation' ? ? 0.291227 -0.819651 0.493315 -0.819651 -0.479699 -0.313149 0.493315 -0.313149 -0.811528 272.86926 688.69316 430.05328 36 'point symmetry operation' ? ? 0.822308 0.480371 -0.305046 0.488988 -0.322345 0.810546 0.291033 -0.815682 -0.499963 0.89977 5.2593 533.611 37 'point symmetry operation' ? ? 0.506686 0.29136 0.811405 -0.322414 -0.808834 0.49177 0.799574 -0.510781 -0.315886 -160.49208 431.72378 270.47288 38 'point symmetry operation' ? ? -0.501515 -0.313051 0.806524 -0.313051 -0.803402 -0.506502 0.806524 -0.506502 0.304917 266.19086 691.15666 103.74796 39 'point symmetry operation' ? ? -0.808995 -0.497587 -0.312944 0.504137 -0.313557 -0.804691 0.302278 -0.808758 0.504518 691.28726 425.03052 263.84441 40 'point symmetry operation' ? ? 0.009172 -0.007225 -0.999932 0.999825 -0.016247 0.009289 -0.016313 -0.999842 0.007075 527.32835 1.12264 529.51439 41 'point symmetry operation' ? ? -0.499699 0.326602 -0.802267 -0.286876 0.811522 0.509053 0.817314 0.484524 -0.311822 521.66171 -8.89653 2.62956 42 'point symmetry operation' ? ? 0.309097 0.811526 -0.495868 -0.803676 0.501669 0.320052 0.508492 0.29959 0.807268 99.56223 259.02537 -162.32752 43 'point symmetry operation' ? ? 0.309025 0.811663 0.495688 -0.809161 0.498266 -0.311431 -0.499762 -0.304851 0.810743 -162.019 427.9497 262.1731 44 'point symmetry operation' ? ? -0.499815 0.326823 0.802104 -0.295751 0.806016 -0.512708 -0.814074 -0.493482 -0.306201 98.41438 264.42878 689.486 45 'point symmetry operation' ? ? -0.999634 0.027039 -0.000076 0.027039 0.999619 -0.005621 -0.000076 -0.005621 -0.999984 520.95229 -5.55704 529.07927 46 'point symmetry operation' ? ? -0.009288 -0.001353 0.999956 -0.999899 0.010741 -0.009273 -0.010728 -0.999941 -0.001453 3.10361 526.98843 530.31534 47 'point symmetry operation' ? ? -0.819769 -0.487359 0.300765 -0.487359 0.31786 -0.813293 0.300765 -0.813293 -0.498091 529.54807 522.86195 529.91822 48 'point symmetry operation' ? ? -0.499815 -0.295751 -0.814074 0.326823 0.806016 -0.493482 0.802104 -0.512708 -0.306201 688.68655 94.95123 267.75737 49 'point symmetry operation' ? ? 0.508408 0.308675 -0.803891 0.317475 0.800594 0.508192 0.800456 -0.513585 0.309032 260.59508 -165.38566 106.13018 50 'point symmetry operation' ? ? 0.811571 0.490623 0.317241 -0.502484 0.309087 0.80745 0.298098 -0.814711 0.497376 -163.11847 101.62801 268.39993 51 'point symmetry operation' ? ? 0.822308 0.488988 0.291033 0.480371 -0.322345 -0.815682 -0.305046 0.810546 -0.499963 -158.60985 436.51998 262.79726 52 'point symmetry operation' ? ? 0.017867 0.006859 0.999817 0.999783 -0.010816 -0.017792 0.010692 0.999918 -0.007051 -6.19315 6.84708 -0.47314 53 'point symmetry operation' ? ? -0.808808 -0.488849 0.326889 0.5094 -0.304648 0.804799 -0.293839 0.817445 0.495422 520.1545 -3.275 -4.55293 54 'point symmetry operation' ? ? -0.515279 -0.313085 -0.797788 -0.313085 -0.797776 0.515297 -0.797788 0.515297 0.313055 693.03854 420.1421 256.19602 55 'point symmetry operation' ? ? 0.492806 0.291252 -0.819948 -0.331026 -0.808713 -0.486215 -0.804714 0.511034 -0.302127 273.5391 691.95035 421.42753 56 'point symmetry operation' ? ? -0.313321 -0.814237 -0.488722 0.806404 -0.499918 0.315902 -0.50154 -0.295129 0.813238 690.14212 98.67951 259.42414 57 'point symmetry operation' ? ? 0.492806 -0.331026 -0.804714 0.291252 -0.808713 0.511034 -0.819948 -0.486215 -0.302127 433.38044 264.55698 688.04875 58 'point symmetry operation' ? ? 0.999598 -0.027063 -0.008503 -0.027063 -0.999634 0.000115 -0.008503 0.000115 -0.999964 9.47555 533.66545 529.78877 59 'point symmetry operation' ? ? 0.506686 -0.322414 0.799574 0.29136 -0.808834 -0.510781 0.811405 0.49177 -0.315886 4.24959 534.10617 3.35412 60 'point symmetry operation' ? ? -0.304742 -0.808914 0.502783 0.806471 -0.499992 -0.315614 0.506692 0.309299 0.804735 424.92467 265.27007 -163.74041 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 E SG CYS 12 E CYS 32 1_555 E SG CYS 94 E CYS 114 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 E SG CYS 35 E CYS 55 1_555 E SG CYS 75 E CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 E SG CYS 64 E CYS 84 1_555 E SG CYS 89 E CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 E SG CYS 102 E CYS 122 1_555 E SG CYS 166 E CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf5 E SG CYS 127 E CYS 147 1_555 E SG CYS 147 E CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 E SG CYS 131 E CYS 151 1_555 E SG CYS 149 E CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 E SG CYS 170 E CYS 190 1_555 E SG CYS 178 E CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 E ND2 ASN 25 E ASN 45 1_555 G C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 E ND2 ASN 39 E ASN 59 1_555 H C1 NAG . E NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 E ND2 ASN 273 E ASN 293 1_555 I C1 NAG . E NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? # _chem_comp.formula 'C18 H37 N O2' _chem_comp.formula_weight 299.492 _chem_comp.id SPH _chem_comp.mon_nstd_flag . _chem_comp.name SPHINGOSINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7BZT _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code F 6 SPH A 1 401 401 SPH SPH . G 7 NAG E 1 401 1324 NAG NAG . H 7 NAG E 1 402 1325 NAG NAG . I 7 NAG E 1 403 1326 NAG NAG . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 SPH . . . F 6 167.774 357.706 280.687 1 19.73 ? C1 SPH 401 A 1 HETATM 2 O O1 SPH . . . F 6 167.247 357.688 279.378 1 19.73 ? O1 SPH 401 A 1 HETATM 3 C C2 SPH . . . F 6 169.223 358.167 280.636 1 19.73 ? C2 SPH 401 A 1 HETATM 4 N N2 SPH . . . F 6 169.448 359.207 281.622 1 19.73 ? N2 SPH 401 A 1 HETATM 5 C C3 SPH . . . F 6 170.186 357.028 280.931 1 19.73 ? C3 SPH 401 A 1 HETATM 6 O O3 SPH . . . F 6 169.866 355.917 280.133 1 19.73 ? O3 SPH 401 A 1 HETATM 7 C C4 SPH . . . F 6 171.583 357.457 280.603 1 19.73 ? C4 SPH 401 A 1 HETATM 8 C C5 SPH . . . F 6 171.929 357.829 279.222 1 19.73 ? C5 SPH 401 A 1 HETATM 9 C C6 SPH . . . F 6 173.362 358.126 278.85 1 19.73 ? C6 SPH 401 A 1 HETATM 10 C C7 SPH . . . F 6 174.086 358.517 280.129 1 19.73 ? C7 SPH 401 A 1 HETATM 11 C C8 SPH . . . F 6 175.489 359.04 279.873 1 19.73 ? C8 SPH 401 A 1 HETATM 12 C C9 SPH . . . F 6 175.975 359.763 281.122 1 19.73 ? C9 SPH 401 A 1 HETATM 13 C C10 SPH . . . F 6 176.434 361.168 280.769 1 19.73 ? C10 SPH 401 A 1 HETATM 14 C C11 SPH . . . F 6 177.238 361.786 281.9 1 19.73 ? C11 SPH 401 A 1 HETATM 15 C C12 SPH . . . F 6 178.121 362.911 281.372 1 19.73 ? C12 SPH 401 A 1 HETATM 16 C C13 SPH . . . F 6 177.297 364.154 281.06 1 19.73 ? C13 SPH 401 A 1 HETATM 17 C C14 SPH . . . F 6 177.537 364.681 279.652 1 19.73 ? C14 SPH 401 A 1 HETATM 18 C C15 SPH . . . F 6 178.048 366.117 279.684 1 19.73 ? C15 SPH 401 A 1 HETATM 19 C C16 SPH . . . F 6 179.524 366.184 280.059 1 19.73 ? C16 SPH 401 A 1 HETATM 20 C C17 SPH . . . F 6 179.921 367.604 280.449 1 19.73 ? C17 SPH 401 A 1 HETATM 21 C C18 SPH . . . F 6 181.379 367.673 280.888 1 19.73 ? C18 SPH 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 22 _model_server_stats.element_count 21 #