data_1B9T # _model_server_result.job_id Fiv3t09Z1KaelfJ_iPKu2g _model_server_result.datetime_utc '2024-11-25 04:39:54' _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 1b9t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":468}' # _entry.id 1B9T # _exptl.entry_id 1B9T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.317 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "1-(4-CARBOXY-2-GUANIDINOPENTYL)-5,5'-DI(HYDROXYMETHYL)PYRROLIDIN-2-ONE" _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 1B9T _cell.length_a 124.5 _cell.length_b 124.5 _cell.length_c 71.412 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1B9T _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 124.5 0 0 3 'crystal symmetry operation' 3_545 -y+1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 62.25 -62.25 0 4 'crystal symmetry operation' 4_555 y+1/2,-x+1/2,z 0 1 0 -1 0 0 0 0 1 62.25 62.25 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 A SG CYS 11 A CYS 87 1_555 A SG CYS 344 A CYS 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 46 A CYS 122 1_555 A SG CYS 51 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf3 A SG CYS 106 A CYS 182 1_555 A SG CYS 153 A CYS 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 A SG CYS 155 A CYS 231 1_555 A SG CYS 160 A CYS 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf5 A SG CYS 201 A CYS 277 1_555 A SG CYS 215 A CYS 291 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf6 A SG CYS 203 A CYS 279 1_555 A SG CYS 213 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 242 A CYS 318 1_555 A SG CYS 261 A CYS 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf8 A SG CYS 348 A CYS 424 1_555 A SG CYS 371 A CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc1 A OE1 GLU 92 A GLU 168 1_555 D CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc2 A OE1 GLU 92 A GLU 168 2_655 D CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc3 A OE1 GLU 92 A GLU 168 4_555 D CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc4 A OE1 GLU 92 A GLU 168 3_545 D CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc5 A O ASP 217 A ASP 293 1_555 C CA CA . A CA 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc6 A O THR 221 A THR 297 1_555 C CA CA . A CA 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? metalc ? metalc7 A OD2 ASP 248 A ASP 324 1_555 C CA CA . A CA 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc8 A O GLY 270 A GLY 346 1_555 C CA CA . A CA 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc9 C CA CA . A CA 500 1_555 F O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc10 C CA CA . A CA 500 1_555 F O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? # _chem_comp.formula 'C14 H18 N4 O5' _chem_comp.formula_weight 322.317 _chem_comp.id RAI _chem_comp.mon_nstd_flag . _chem_comp.name "1-(4-CARBOXY-2-GUANIDINOPENTYL)-5,5'-DI(HYDROXYMETHYL)PYRROLIDIN-2-ONE" _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 C1 C2 RAI doub 307 n y C1 C6 RAI sing 308 n y C1 H1 RAI sing 309 n n C2 C3 RAI sing 310 n y C2 N15 RAI sing 311 n n C3 C4 RAI doub 312 n y C3 N12 RAI sing 313 n n C4 C5 RAI sing 314 n y C4 H4 RAI sing 315 n n C5 C6 RAI doub 316 n y C5 C10 RAI sing 317 n n C6 H6 RAI sing 318 n n C10 O11 RAI sing 319 n n C10 O32 RAI doub 320 n n O11 H11 RAI sing 321 n n N12 C13 RAI sing 322 n n N12 H12 RAI sing 323 n n C13 N14 RAI sing 324 n n C13 N33 RAI doub 325 n n N14 H141 RAI sing 326 n n N14 H142 RAI sing 327 n n N15 C16 RAI sing 328 n n N15 C19 RAI sing 329 n n C16 C17 RAI sing 330 n n C16 C24 RAI sing 331 n n C16 C28 RAI sing 332 n n C17 C18 RAI sing 333 n n C17 H171 RAI sing 334 n n C17 H172 RAI sing 335 n n C18 C19 RAI sing 336 n n C18 H181 RAI sing 337 n n C18 H182 RAI sing 338 n n C19 O34 RAI doub 339 n n C24 O25 RAI sing 340 n n C24 H241 RAI sing 341 n n C24 H242 RAI sing 342 n n O25 H25 RAI sing 343 n n C28 O29 RAI sing 344 n n C28 H281 RAI sing 345 n n C28 H282 RAI sing 346 n n O29 H29 RAI sing 347 n n N33 H33 RAI sing 348 n n # _atom_sites.entry_id 1B9T _atom_sites.fract_transf_matrix[1][1] 0.008032 _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] 0.008032 _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] 0.014003 _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 B 2 NAG A 1 467 467 NAG NAG . C 3 CA A 1 500 500 CA CA . D 3 CA A 1 501 501 CA CA . E 4 RAI A 1 468 1 RAI RAI . F 5 HOH A 1 502 502 HOH HOH . F 5 HOH A 2 503 503 HOH HOH . F 5 HOH A 3 579 579 HOH HOH . F 5 HOH A 4 586 586 HOH HOH . F 5 HOH A 5 588 588 HOH HOH . F 5 HOH A 6 593 593 HOH HOH . F 5 HOH A 7 594 594 HOH HOH . F 5 HOH A 8 595 595 HOH HOH . F 5 HOH A 9 601 601 HOH HOH . F 5 HOH A 10 602 602 HOH HOH . F 5 HOH A 11 603 603 HOH HOH . F 5 HOH A 12 604 604 HOH HOH . F 5 HOH A 13 605 605 HOH HOH . F 5 HOH A 14 609 609 HOH HOH . F 5 HOH A 15 610 610 HOH HOH . F 5 HOH A 16 611 611 HOH HOH . F 5 HOH A 17 613 613 HOH HOH . F 5 HOH A 18 618 618 HOH HOH . F 5 HOH A 19 620 620 HOH HOH . F 5 HOH A 20 621 621 HOH HOH . F 5 HOH A 21 622 622 HOH HOH . F 5 HOH A 22 623 623 HOH HOH . F 5 HOH A 23 629 629 HOH HOH . F 5 HOH A 24 637 637 HOH HOH . F 5 HOH A 25 638 638 HOH HOH . F 5 HOH A 26 640 640 HOH HOH . F 5 HOH A 27 641 641 HOH HOH . F 5 HOH A 28 642 642 HOH HOH . F 5 HOH A 29 643 643 HOH HOH . F 5 HOH A 30 646 646 HOH HOH . F 5 HOH A 31 649 649 HOH HOH . F 5 HOH A 32 650 650 HOH HOH . F 5 HOH A 33 651 651 HOH HOH . F 5 HOH A 34 652 652 HOH HOH . F 5 HOH A 35 667 667 HOH HOH . F 5 HOH A 36 668 668 HOH HOH . F 5 HOH A 37 672 672 HOH HOH . F 5 HOH A 38 673 673 HOH HOH . F 5 HOH A 39 682 682 HOH HOH . F 5 HOH A 40 683 683 HOH HOH . F 5 HOH A 41 684 684 HOH HOH . F 5 HOH A 42 694 694 HOH HOH . F 5 HOH A 43 697 697 HOH HOH . F 5 HOH A 44 698 698 HOH HOH . F 5 HOH A 45 700 700 HOH HOH . F 5 HOH A 46 706 706 HOH HOH . F 5 HOH A 47 707 707 HOH HOH . F 5 HOH A 48 708 708 HOH HOH . F 5 HOH A 49 709 709 HOH HOH . F 5 HOH A 50 710 710 HOH HOH . F 5 HOH A 51 713 713 HOH HOH . F 5 HOH A 52 715 715 HOH HOH . F 5 HOH A 53 716 716 HOH HOH . F 5 HOH A 54 724 724 HOH HOH . F 5 HOH A 55 726 726 HOH HOH . F 5 HOH A 56 727 727 HOH HOH . F 5 HOH A 57 729 729 HOH HOH . F 5 HOH A 58 730 730 HOH HOH . F 5 HOH A 59 735 735 HOH HOH . F 5 HOH A 60 736 736 HOH HOH . F 5 HOH A 61 737 737 HOH HOH . F 5 HOH A 62 741 741 HOH HOH . F 5 HOH A 63 742 742 HOH HOH . F 5 HOH A 64 755 755 HOH HOH . F 5 HOH A 65 757 757 HOH HOH . F 5 HOH A 66 758 758 HOH HOH . F 5 HOH A 67 767 767 HOH HOH . F 5 HOH A 68 770 770 HOH HOH . F 5 HOH A 69 774 774 HOH HOH . F 5 HOH A 70 779 779 HOH HOH . F 5 HOH A 71 780 780 HOH HOH . F 5 HOH A 72 781 781 HOH HOH . F 5 HOH A 73 793 793 HOH HOH . F 5 HOH A 74 798 798 HOH HOH . F 5 HOH A 75 800 800 HOH HOH . F 5 HOH A 76 816 816 HOH HOH . F 5 HOH A 77 817 817 HOH HOH . F 5 HOH A 78 825 825 HOH HOH . F 5 HOH A 79 828 828 HOH HOH . F 5 HOH A 80 830 830 HOH HOH . F 5 HOH A 81 850 850 HOH HOH . F 5 HOH A 82 852 852 HOH HOH . F 5 HOH A 83 854 854 HOH HOH . F 5 HOH A 84 865 865 HOH HOH . F 5 HOH A 85 866 866 HOH HOH . F 5 HOH A 86 884 884 HOH HOH . F 5 HOH A 87 887 887 HOH HOH . F 5 HOH A 88 890 890 HOH HOH . F 5 HOH A 89 891 891 HOH HOH . F 5 HOH A 90 892 892 HOH HOH . F 5 HOH A 91 896 896 HOH HOH . F 5 HOH A 92 903 903 HOH HOH . F 5 HOH A 93 905 905 HOH HOH . F 5 HOH A 94 910 910 HOH HOH . F 5 HOH A 95 914 914 HOH HOH . F 5 HOH A 96 917 917 HOH HOH . F 5 HOH A 97 921 921 HOH HOH . F 5 HOH A 98 930 930 HOH HOH . F 5 HOH A 99 931 931 HOH HOH . F 5 HOH A 100 934 934 HOH HOH . F 5 HOH A 101 935 935 HOH HOH . F 5 HOH A 102 943 943 HOH HOH . F 5 HOH A 103 955 955 HOH HOH . F 5 HOH A 104 956 956 HOH HOH . F 5 HOH A 105 957 957 HOH HOH . F 5 HOH A 106 961 961 HOH HOH . F 5 HOH A 107 963 963 HOH HOH . F 5 HOH A 108 966 966 HOH HOH . F 5 HOH A 109 967 967 HOH HOH . F 5 HOH A 110 968 968 HOH HOH . F 5 HOH A 111 969 969 HOH HOH . F 5 HOH A 112 970 970 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 C C1 RAI . . . E 4 33.835 -9.719 64.605 1 14.82 ? C1 RAI 468 A 1 HETATM 2 C C2 RAI . . . E 4 32.53 -9.464 64.087 1 20.34 ? C2 RAI 468 A 1 HETATM 3 C C3 RAI . . . E 4 31.46 -10.344 64.457 1 21.91 ? C3 RAI 468 A 1 HETATM 4 C C4 RAI . . . E 4 31.701 -11.443 65.309 1 20.09 ? C4 RAI 468 A 1 HETATM 5 C C5 RAI . . . E 4 32.986 -11.7 65.815 1 21.17 ? C5 RAI 468 A 1 HETATM 6 C C6 RAI . . . E 4 34.063 -10.825 65.459 1 19.83 ? C6 RAI 468 A 1 HETATM 7 C C10 RAI . . . E 4 33.209 -12.862 66.694 1 20.41 ? C10 RAI 468 A 1 HETATM 8 O O11 RAI . . . E 4 32.125 -13.62 66.952 1 26.66 ? O11 RAI 468 A 1 HETATM 9 N N12 RAI . . . E 4 30.179 -10.161 64.013 1 19.28 ? N12 RAI 468 A 1 HETATM 10 C C13 RAI . . . E 4 29.299 -11.045 63.512 1 27.47 ? C13 RAI 468 A 1 HETATM 11 N N14 RAI . . . E 4 29.733 -12.173 62.909 1 25.71 ? N14 RAI 468 A 1 HETATM 12 N N15 RAI . . . E 4 32.274 -8.376 63.237 1 26.07 ? N15 RAI 468 A 1 HETATM 13 C C16 RAI . . . E 4 32.445 -8.352 61.731 1 19.46 ? C16 RAI 468 A 1 HETATM 14 C C17 RAI . . . E 4 32.202 -6.847 61.401 1 16.19 ? C17 RAI 468 A 1 HETATM 15 C C18 RAI . . . E 4 31.58 -6.186 62.627 1 15.09 ? C18 RAI 468 A 1 HETATM 16 C C19 RAI . . . E 4 31.799 -7.196 63.73 1 22.02 ? C19 RAI 468 A 1 HETATM 17 C C24 RAI . . . E 4 31.367 -9.238 61.021 1 20.44 ? C24 RAI 468 A 1 HETATM 18 O O25 RAI . . . E 4 31.67 -9.445 59.641 1 30.97 ? O25 RAI 468 A 1 HETATM 19 C C28 RAI . . . E 4 33.876 -8.844 61.288 1 18.55 ? C28 RAI 468 A 1 HETATM 20 O O29 RAI . . . E 4 34.443 -7.965 60.361 1 28.2 ? O29 RAI 468 A 1 HETATM 21 O O32 RAI . . . E 4 34.281 -13.11 67.14 1 21.4 ? O32 RAI 468 A 1 HETATM 22 N N33 RAI . . . E 4 27.997 -10.78 63.621 1 32.01 ? N33 RAI 468 A 1 HETATM 23 O O34 RAI . . . E 4 31.558 -6.948 64.906 1 28.03 ? O34 RAI 468 A 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 23 #