data_7D7O # _model_server_result.job_id wpCLdrLLihkeIu6CGfOp2Q _model_server_result.datetime_utc '2025-03-09 01:54:29' _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 7d7o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 7D7O # _exptl.entry_id 7D7O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _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 90 _cell.angle_gamma 90 _cell.entry_id 7D7O _cell.length_a 116.708 _cell.length_b 116.708 _cell.length_c 147.794 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7D7O _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details PISA _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,G,H,I,J,K,L,M,N,O _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 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 I N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NZ _struct_conn.ptnr1_label_comp_id LYS _struct_conn.ptnr1_label_seq_id 195 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id LYS _struct_conn.ptnr1_auth_seq_id 195 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id C _struct_conn.ptnr2_label_atom_id C4A _struct_conn.ptnr2_label_comp_id PLP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id PLP _struct_conn.ptnr2_auth_seq_id 401 _struct_conn.ptnr2_symmetry 1_555 _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 1.287 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 N1 C2 PLP doub 260 n y N1 C6 PLP sing 261 n y C2 C2A PLP sing 262 n n C2 C3 PLP sing 263 n y C2A H2A1 PLP sing 264 n n C2A H2A2 PLP sing 265 n n C2A H2A3 PLP sing 266 n n C3 O3 PLP sing 267 n n C3 C4 PLP doub 268 n y O3 HO3 PLP sing 269 n n C4 C4A PLP sing 270 n n C4 C5 PLP sing 271 n y C4A O4A PLP doub 272 n n C4A H4A PLP sing 273 n n C5 C6 PLP doub 274 n y C5 C5A PLP sing 275 n n C6 H6 PLP sing 276 n n C5A O4P PLP sing 277 n n C5A H5A1 PLP sing 278 n n C5A H5A2 PLP sing 279 n n O4P P PLP sing 280 n n P O1P PLP doub 281 n n P O2P PLP sing 282 n n P O3P PLP sing 283 n n O2P HOP2 PLP sing 284 n n O3P HOP3 PLP sing 285 n n # _atom_sites.entry_id 7D7O _atom_sites.fract_transf_matrix[1][1] 0.008568 _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] 0.008568 _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] 0.006766 _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 PLP A 1 401 401 PLP PLP . D 3 GOL A 1 402 501 GOL GOL . E 3 GOL A 1 403 701 GOL GOL . F 3 GOL A 1 404 801 GOL GOL . G 4 SO4 A 1 405 1 SO4 SO4 . H 4 SO4 A 1 406 5 SO4 SO4 . I 2 PLP B 1 401 401 PLP PLP . J 3 GOL B 1 402 501 GOL GOL . K 3 GOL B 1 403 701 GOL GOL . L 4 SO4 B 1 404 3 SO4 SO4 . M 4 SO4 B 1 405 4 SO4 SO4 . N 5 HOH A 1 501 70 HOH HOH . N 5 HOH A 2 502 89 HOH HOH . N 5 HOH A 3 503 57 HOH HOH . N 5 HOH A 4 504 67 HOH HOH . N 5 HOH A 5 505 53 HOH HOH . N 5 HOH A 6 506 85 HOH HOH . N 5 HOH A 7 507 72 HOH HOH . N 5 HOH A 8 508 139 HOH HOH . N 5 HOH A 9 509 91 HOH HOH . N 5 HOH A 10 510 68 HOH HOH . N 5 HOH A 11 511 66 HOH HOH . N 5 HOH A 12 512 69 HOH HOH . N 5 HOH A 13 513 97 HOH HOH . N 5 HOH A 14 514 87 HOH HOH . N 5 HOH A 15 515 58 HOH HOH . N 5 HOH A 16 516 101 HOH HOH . N 5 HOH A 17 517 63 HOH HOH . N 5 HOH A 18 518 11 HOH HOH . N 5 HOH A 19 519 135 HOH HOH . N 5 HOH A 20 520 49 HOH HOH . N 5 HOH A 21 521 48 HOH HOH . N 5 HOH A 22 522 62 HOH HOH . N 5 HOH A 23 523 114 HOH HOH . N 5 HOH A 24 524 22 HOH HOH . N 5 HOH A 25 525 18 HOH HOH . N 5 HOH A 26 526 64 HOH HOH . N 5 HOH A 27 527 15 HOH HOH . N 5 HOH A 28 528 52 HOH HOH . N 5 HOH A 29 529 78 HOH HOH . N 5 HOH A 30 530 38 HOH HOH . N 5 HOH A 31 531 79 HOH HOH . N 5 HOH A 32 532 59 HOH HOH . N 5 HOH A 33 533 140 HOH HOH . N 5 HOH A 34 534 80 HOH HOH . N 5 HOH A 35 535 13 HOH HOH . N 5 HOH A 36 536 5 HOH HOH . N 5 HOH A 37 537 47 HOH HOH . N 5 HOH A 38 538 50 HOH HOH . N 5 HOH A 39 539 71 HOH HOH . N 5 HOH A 40 540 54 HOH HOH . N 5 HOH A 41 541 77 HOH HOH . N 5 HOH A 42 542 82 HOH HOH . N 5 HOH A 43 543 23 HOH HOH . N 5 HOH A 44 544 16 HOH HOH . N 5 HOH A 45 545 81 HOH HOH . N 5 HOH A 46 546 116 HOH HOH . N 5 HOH A 47 547 34 HOH HOH . N 5 HOH A 48 548 86 HOH HOH . N 5 HOH A 49 549 100 HOH HOH . N 5 HOH A 50 550 12 HOH HOH . N 5 HOH A 51 551 36 HOH HOH . N 5 HOH A 52 552 27 HOH HOH . N 5 HOH A 53 553 40 HOH HOH . N 5 HOH A 54 554 9 HOH HOH . N 5 HOH A 55 555 74 HOH HOH . N 5 HOH A 56 556 90 HOH HOH . N 5 HOH A 57 557 73 HOH HOH . N 5 HOH A 58 558 61 HOH HOH . N 5 HOH A 59 559 56 HOH HOH . N 5 HOH A 60 560 134 HOH HOH . N 5 HOH A 61 561 136 HOH HOH . N 5 HOH A 62 562 94 HOH HOH . N 5 HOH A 63 563 125 HOH HOH . N 5 HOH A 64 564 130 HOH HOH . N 5 HOH A 65 565 75 HOH HOH . N 5 HOH A 66 566 60 HOH HOH . N 5 HOH A 67 567 65 HOH HOH . N 5 HOH A 68 568 46 HOH HOH . N 5 HOH A 69 569 84 HOH HOH . N 5 HOH A 70 570 83 HOH HOH . N 5 HOH A 71 571 88 HOH HOH . N 5 HOH A 72 572 29 HOH HOH . N 5 HOH A 73 573 30 HOH HOH . N 5 HOH A 74 574 76 HOH HOH . N 5 HOH A 75 575 44 HOH HOH . N 5 HOH A 76 576 28 HOH HOH . N 5 HOH A 77 577 138 HOH HOH . N 5 HOH A 78 578 137 HOH HOH . N 5 HOH A 79 579 126 HOH HOH . O 5 HOH B 1 501 106 HOH HOH . O 5 HOH B 2 502 99 HOH HOH . O 5 HOH B 3 503 108 HOH HOH . O 5 HOH B 4 504 129 HOH HOH . O 5 HOH B 5 505 103 HOH HOH . O 5 HOH B 6 506 133 HOH HOH . O 5 HOH B 7 507 93 HOH HOH . O 5 HOH B 8 508 107 HOH HOH . O 5 HOH B 9 509 102 HOH HOH . O 5 HOH B 10 510 131 HOH HOH . O 5 HOH B 11 511 24 HOH HOH . O 5 HOH B 12 512 141 HOH HOH . O 5 HOH B 13 513 43 HOH HOH . O 5 HOH B 14 514 35 HOH HOH . O 5 HOH B 15 515 41 HOH HOH . O 5 HOH B 16 516 120 HOH HOH . O 5 HOH B 17 517 51 HOH HOH . O 5 HOH B 18 518 110 HOH HOH . O 5 HOH B 19 519 124 HOH HOH . O 5 HOH B 20 520 118 HOH HOH . O 5 HOH B 21 521 123 HOH HOH . O 5 HOH B 22 522 7 HOH HOH . O 5 HOH B 23 523 55 HOH HOH . O 5 HOH B 24 524 42 HOH HOH . O 5 HOH B 25 525 122 HOH HOH . O 5 HOH B 26 526 95 HOH HOH . O 5 HOH B 27 527 109 HOH HOH . O 5 HOH B 28 528 14 HOH HOH . O 5 HOH B 29 529 98 HOH HOH . O 5 HOH B 30 530 128 HOH HOH . O 5 HOH B 31 531 17 HOH HOH . O 5 HOH B 32 532 25 HOH HOH . O 5 HOH B 33 533 104 HOH HOH . O 5 HOH B 34 534 117 HOH HOH . O 5 HOH B 35 535 1 HOH HOH . O 5 HOH B 36 536 105 HOH HOH . O 5 HOH B 37 537 6 HOH HOH . O 5 HOH B 38 538 19 HOH HOH . O 5 HOH B 39 539 121 HOH HOH . O 5 HOH B 40 540 37 HOH HOH . O 5 HOH B 41 541 113 HOH HOH . O 5 HOH B 42 542 119 HOH HOH . O 5 HOH B 43 543 115 HOH HOH . O 5 HOH B 44 544 21 HOH HOH . O 5 HOH B 45 545 8 HOH HOH . O 5 HOH B 46 546 112 HOH HOH . O 5 HOH B 47 547 127 HOH HOH . O 5 HOH B 48 548 111 HOH HOH . O 5 HOH B 49 549 96 HOH HOH . O 5 HOH B 50 550 39 HOH HOH . O 5 HOH B 51 551 33 HOH HOH . O 5 HOH B 52 552 132 HOH HOH . O 5 HOH B 53 553 92 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 N N1 PLP . . . I 2 -4.289 29.987 -8.562 1 60.67 ? N1 PLP 401 B 1 HETATM 2 C C2 PLP . . . I 2 -4.609 29.195 -9.589 1 65.83 ? C2 PLP 401 B 1 HETATM 3 C C2A PLP . . . I 2 -4.858 29.801 -10.935 1 64.81 ? C2A PLP 401 B 1 HETATM 4 C C3 PLP . . . I 2 -4.711 27.805 -9.399 1 72.52 ? C3 PLP 401 B 1 HETATM 5 O O3 PLP . . . I 2 -5.039 27.034 -10.472 1 65.32 ? O3 PLP 401 B 1 HETATM 6 C C4 PLP . . . I 2 -4.487 27.266 -8.105 1 81.67 ? C4 PLP 401 B 1 HETATM 7 C C4A PLP . . . I 2 -4.621 25.829 -7.847 1 93.99 ? C4A PLP 401 B 1 HETATM 8 O O4A PLP . . . I 2 -5.313 25.058 -8.477 1 115.84 ? O4A PLP 401 B 1 HETATM 9 C C5 PLP . . . I 2 -4.132 28.119 -7.044 1 65.8 ? C5 PLP 401 B 1 HETATM 10 C C6 PLP . . . I 2 -4.062 29.463 -7.328 1 67.51 ? C6 PLP 401 B 1 HETATM 11 C C5A PLP . . . I 2 -3.877 27.584 -5.647 1 57.72 ? C5A PLP 401 B 1 HETATM 12 O O4P PLP . . . I 2 -2.554 26.979 -5.4 1 44.11 ? O4P PLP 401 B 1 HETATM 13 P P PLP . . . I 2 -2.174 25.832 -4.296 1 35.13 ? P PLP 401 B 1 HETATM 14 O O1P PLP . . . I 2 -2.958 24.607 -4.641 1 34.99 ? O1P PLP 401 B 1 HETATM 15 O O2P PLP . . . I 2 -0.677 25.602 -4.408 1 33.98 ? O2P PLP 401 B 1 HETATM 16 O O3P PLP . . . I 2 -2.542 26.402 -2.95 1 36.43 ? O3P PLP 401 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 214 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 16 #