data_5UXH # _model_server_result.job_id ylhrEIlilEhs1JWFzXiPHw _model_server_result.datetime_utc '2024-10-12 16:37:24' _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 5uxh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5UXH # _exptl.entry_id 5UXH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 589.342 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 104.13 _cell.angle_gamma 90 _cell.entry_id 5UXH _cell.length_a 50.23 _cell.length_b 133.92 _cell.length_c 70.01 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5UXH _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 A SG CYS 15 A CYS 38 1_555 A SG CYS 17 A CYS 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 103 A CYS 126 1_555 A SG CYS 117 A CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 226 A CYS 249 1_555 A SG CYS 260 A CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 A SG CYS 244 A CYS 267 1_555 A SG CYS 331 A CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 B SG CYS 15 B CYS 38 1_555 B SG CYS 17 B CYS 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 B SG CYS 103 B CYS 126 1_555 B SG CYS 117 B CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 B SG CYS 226 B CYS 249 1_555 B SG CYS 260 B CYS 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf8 B SG CYS 244 B CYS 267 1_555 B SG CYS 331 B CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? covale ? covale1 A ND2 ASN 39 A ASN 62 1_555 D C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale2 B ND2 ASN 39 B ASN 62 1_555 F C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? # _chem_comp.formula 'C16 H25 N5 O15 P2' _chem_comp.formula_weight 589.342 _chem_comp.id GFB _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag P O1P GFB sing 83 n n O1P HO1P GFB sing 84 n n O3P P GFB doub 85 n n P O5' GFB sing 86 n n P O2P GFB sing 87 n n O2P P1 GFB sing 88 n n O5' C5' GFB sing 89 n n O1 P1 GFB sing 90 n n O1X P1 GFB doub 91 n n P1 O2X GFB sing 92 n n C4' C5' GFB sing 93 n n C5' "H5'A" GFB sing 94 n n C5' H5' GFB sing 95 n n H4' C4' GFB sing 96 n n C3' C4' GFB sing 97 n n C4' O4' GFB sing 98 n n O4' C1' GFB sing 99 n n O3' C3' GFB sing 100 n n C3' C2' GFB sing 101 n n C3' H3' GFB sing 102 n n C2' C1' GFB sing 103 n n H1' C1' GFB sing 104 n n C1' N9 GFB sing 105 n n HO3' O3' GFB sing 106 n n O2' C2' GFB sing 107 n n C2' H2' GFB sing 108 n n O2' HO2' GFB sing 109 n n N9 C4 GFB sing 110 n y N9 C8 GFB sing 111 n y H8 C8 GFB sing 112 n n C8 N7 GFB doub 113 n y N3 C4 GFB sing 114 n n C4 C5 GFB doub 115 n y C5 N7 GFB sing 116 n y C5 C6 GFB sing 117 n n N1 C6 GFB sing 118 n n C6 O6 GFB doub 119 n n C2 N1 GFB sing 120 n n N1 HN1 GFB sing 121 n n N3 C2 GFB doub 122 n n N2 C2 GFB sing 123 n n HN2 N2 GFB sing 124 n n N2 HN2A GFB sing 125 n n C2A C1 GFB sing 126 n n C1 O5 GFB sing 127 n n C1 H1 GFB sing 128 n n C1 O1 GFB sing 129 n n C3 C2A GFB sing 130 n n O2 C2A GFB sing 131 n n H2A C2A GFB sing 132 n n C5A O5 GFB sing 133 n n O3 C3 GFB sing 134 n n C3 H3 GFB sing 135 n n C3 C4A GFB sing 136 n n HO2 O2 GFB sing 137 n n H4A C4A GFB sing 138 n n O4 C4A GFB sing 139 n n C4A C5A GFB sing 140 n n HO3 O3 GFB sing 141 n n C5A H5A GFB sing 142 n n C5A C6A GFB sing 143 n n O4 HO4 GFB sing 144 n n H6A C6A GFB sing 145 n n H6AA C6A GFB sing 146 n n C6A H6AB GFB sing 147 n n O2X HO2X GFB sing 148 n n # _atom_sites.entry_id 5UXH _atom_sites.fract_transf_matrix[1][1] 0.019908 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005013 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007467 _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] 0.01473 _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 C 2 GFB A 1 401 1 GFB GFB . D 3 NAG A 1 402 62 NAG NAG . E 2 GFB B 1 401 1 GFB GFB . F 3 NAG B 1 402 62 NAG NAG . G 4 HOH A 1 501 16 HOH HOH . G 4 HOH A 2 502 60 HOH HOH . G 4 HOH A 3 503 32 HOH HOH . G 4 HOH A 4 504 66 HOH HOH . G 4 HOH A 5 505 33 HOH HOH . G 4 HOH A 6 506 18 HOH HOH . G 4 HOH A 7 507 72 HOH HOH . G 4 HOH A 8 508 26 HOH HOH . G 4 HOH A 9 509 43 HOH HOH . G 4 HOH A 10 510 41 HOH HOH . G 4 HOH A 11 511 2 HOH HOH . G 4 HOH A 12 512 11 HOH HOH . G 4 HOH A 13 513 55 HOH HOH . G 4 HOH A 14 514 6 HOH HOH . G 4 HOH A 15 515 56 HOH HOH . G 4 HOH A 16 516 58 HOH HOH . G 4 HOH A 17 517 9 HOH HOH . G 4 HOH A 18 518 19 HOH HOH . G 4 HOH A 19 519 17 HOH HOH . G 4 HOH A 20 520 29 HOH HOH . G 4 HOH A 21 521 38 HOH HOH . G 4 HOH A 22 522 44 HOH HOH . G 4 HOH A 23 523 42 HOH HOH . G 4 HOH A 24 524 68 HOH HOH . G 4 HOH A 25 525 71 HOH HOH . G 4 HOH A 26 526 39 HOH HOH . G 4 HOH A 27 527 53 HOH HOH . G 4 HOH A 28 528 12 HOH HOH . G 4 HOH A 29 529 48 HOH HOH . G 4 HOH A 30 530 52 HOH HOH . G 4 HOH A 31 531 23 HOH HOH . G 4 HOH A 32 532 54 HOH HOH . G 4 HOH A 33 533 35 HOH HOH . G 4 HOH A 34 534 50 HOH HOH . G 4 HOH A 35 535 27 HOH HOH . G 4 HOH A 36 536 65 HOH HOH . H 4 HOH B 1 501 69 HOH HOH . H 4 HOH B 2 502 63 HOH HOH . H 4 HOH B 3 503 47 HOH HOH . H 4 HOH B 4 504 22 HOH HOH . H 4 HOH B 5 505 14 HOH HOH . H 4 HOH B 6 506 21 HOH HOH . H 4 HOH B 7 507 8 HOH HOH . H 4 HOH B 8 508 5 HOH HOH . H 4 HOH B 9 509 59 HOH HOH . H 4 HOH B 10 510 10 HOH HOH . H 4 HOH B 11 511 73 HOH HOH . H 4 HOH B 12 512 1 HOH HOH . H 4 HOH B 13 513 7 HOH HOH . H 4 HOH B 14 514 25 HOH HOH . H 4 HOH B 15 515 20 HOH HOH . H 4 HOH B 16 516 51 HOH HOH . H 4 HOH B 17 517 57 HOH HOH . H 4 HOH B 18 518 28 HOH HOH . H 4 HOH B 19 519 31 HOH HOH . H 4 HOH B 20 520 70 HOH HOH . H 4 HOH B 21 521 36 HOH HOH . H 4 HOH B 22 522 15 HOH HOH . H 4 HOH B 23 523 3 HOH HOH . H 4 HOH B 24 524 4 HOH HOH . H 4 HOH B 25 525 13 HOH HOH . H 4 HOH B 26 526 37 HOH HOH . H 4 HOH B 27 527 34 HOH HOH . H 4 HOH B 28 528 45 HOH HOH . H 4 HOH B 29 529 62 HOH HOH . H 4 HOH B 30 530 49 HOH HOH . H 4 HOH B 31 531 46 HOH HOH . H 4 HOH B 32 532 64 HOH HOH . H 4 HOH B 33 533 40 HOH HOH . H 4 HOH B 34 534 61 HOH HOH . H 4 HOH B 35 535 24 HOH HOH . H 4 HOH B 36 536 67 HOH HOH . # 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 O O1P GFB . . . C 2 -5.734 -51.919 78.306 1 63.86 ? O1P GFB 401 A 1 HETATM 2 P P GFB . . . C 2 -4.834 -50.962 77.583 1 56.72 ? P GFB 401 A 1 HETATM 3 O O3P GFB . . . C 2 -4.893 -49.57 78.242 1 50.07 ? O3P GFB 401 A 1 HETATM 4 O O2P GFB . . . C 2 -5.284 -50.848 76.052 1 58.25 ? O2P GFB 401 A 1 HETATM 5 O O5' GFB . . . C 2 -3.337 -51.526 77.641 1 60.5 ? O5' GFB 401 A 1 HETATM 6 P P1 GFB . . . C 2 -4.995 -52.054 75.042 1 51.02 ? P1 GFB 401 A 1 HETATM 7 C C5' GFB . . . C 2 -2.295 -50.82 76.983 1 60.59 ? C5' GFB 401 A 1 HETATM 8 C C4' GFB . . . C 2 -1.41 -50.17 78.031 1 58.87 ? C4' GFB 401 A 1 HETATM 9 O O4' GFB . . . C 2 -0.085 -49.96 77.484 1 62 ? O4' GFB 401 A 1 HETATM 10 C C3' GFB . . . C 2 -1.923 -48.803 78.444 1 49.27 ? C3' GFB 401 A 1 HETATM 11 C C1' GFB . . . C 2 0.337 -48.618 77.692 1 57.7 ? C1' GFB 401 A 1 HETATM 12 O O3' GFB . . . C 2 -2.673 -48.898 79.654 1 50.56 ? O3' GFB 401 A 1 HETATM 13 C C2' GFB . . . C 2 -0.667 -47.976 78.631 1 53.65 ? C2' GFB 401 A 1 HETATM 14 O O2' GFB . . . C 2 -0.178 -48.113 79.967 1 45.71 ? O2' GFB 401 A 1 HETATM 15 N N9 GFB . . . C 2 0.303 -47.91 76.395 1 58.58 ? N9 GFB 401 A 1 HETATM 16 C C8 GFB . . . C 2 -0.1 -48.444 75.199 1 56.78 ? C8 GFB 401 A 1 HETATM 17 C C4 GFB . . . C 2 0.66 -46.609 76.183 1 55.63 ? C4 GFB 401 A 1 HETATM 18 N N7 GFB . . . C 2 0.007 -47.495 74.248 1 55.6 ? N7 GFB 401 A 1 HETATM 19 C C5 GFB . . . C 2 0.482 -46.343 74.853 1 57.64 ? C5 GFB 401 A 1 HETATM 20 C C6 GFB . . . C 2 0.805 -44.983 74.364 1 66.21 ? C6 GFB 401 A 1 HETATM 21 O O6 GFB . . . C 2 0.661 -44.678 73.164 1 66.87 ? O6 GFB 401 A 1 HETATM 22 N N1 GFB . . . C 2 1.267 -44.065 75.267 1 73.21 ? N1 GFB 401 A 1 HETATM 23 C C2 GFB . . . C 2 1.418 -44.393 76.557 1 60.01 ? C2 GFB 401 A 1 HETATM 24 N N2 GFB . . . C 2 1.874 -43.463 77.425 1 54.86 ? N2 GFB 401 A 1 HETATM 25 N N3 GFB . . . C 2 1.126 -45.63 77.014 1 56.34 ? N3 GFB 401 A 1 HETATM 26 C C1 GFB . . . C 2 -4.402 -54.441 75.964 1 60.31 ? C1 GFB 401 A 1 HETATM 27 C C2A GFB . . . C 2 -4.336 -54.684 77.466 1 59.38 ? C2A GFB 401 A 1 HETATM 28 O O1 GFB . . . C 2 -4.015 -53.091 75.74 1 71.4 ? O1 GFB 401 A 1 HETATM 29 O O5 GFB . . . C 2 -3.494 -55.279 75.255 1 55.83 ? O5 GFB 401 A 1 HETATM 30 C C3 GFB . . . C 2 -4.311 -56.155 77.857 1 59.97 ? C3 GFB 401 A 1 HETATM 31 O O2 GFB . . . C 2 -5.479 -54.071 78.063 1 67.42 ? O2 GFB 401 A 1 HETATM 32 C C4A GFB . . . C 2 -3.365 -56.939 76.969 1 55.08 ? C4A GFB 401 A 1 HETATM 33 O O3 GFB . . . C 2 -3.868 -56.273 79.211 1 63.41 ? O3 GFB 401 A 1 HETATM 34 C C5A GFB . . . C 2 -3.696 -56.662 75.508 1 60.72 ? C5A GFB 401 A 1 HETATM 35 O O4 GFB . . . C 2 -2.027 -56.528 77.25 1 55.56 ? O4 GFB 401 A 1 HETATM 36 C C6A GFB . . . C 2 -2.815 -57.485 74.579 1 55.99 ? C6A GFB 401 A 1 HETATM 37 O O1X GFB . . . C 2 -6.281 -52.749 74.705 1 70.76 ? O1X GFB 401 A 1 HETATM 38 O O2X GFB . . . C 2 -4.357 -51.531 73.792 1 58.52 ? O2X GFB 401 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 38 #