data_7NWM # _model_server_result.job_id WAxmYklCzNwsc-WNSwBH7w _model_server_result.datetime_utc '2024-12-04 15:04:09' _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 7nwm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 7NWM # _exptl.entry_id 7NWM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _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 7NWM _cell.length_a 66.3 _cell.length_b 103.839 _cell.length_c 107.816 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NWM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 3 D N N ? 3 F 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 338 A CYS 335 1_555 A SG CYS 341 A CYS 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 338 B CYS 335 1_555 B SG CYS 341 B CYS 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? covale ? covale1 A NZ LYS 225 A LYS 222 1_555 D C4A PLP . A PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.279 ? covale ? covale2 B NZ LYS 225 B LYS 222 1_555 F C4A PLP . B PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.292 ? metalc ? metalc1 B OD2 ASP 136 B ASP 133 1_555 G MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc2 G MG MG . B MG 403 1_555 I O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc3 G MG MG . B MG 403 1_555 I O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc4 G MG MG . B MG 403 1_555 I O HOH . B HOH 509 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc5 G MG MG . B MG 403 1_555 I O HOH . B HOH 549 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? # _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 7NWM _atom_sites.fract_transf_matrix[1][1] 0.015083 _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] 0.00963 _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] 0.009275 _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 UTN A 1 401 401 UTN LIG . D 3 PLP A 1 402 420 PLP PLP . E 2 UTN B 1 401 401 UTN LIG . F 3 PLP B 1 402 420 PLP PLP . G 4 MG B 1 403 430 MG MG . H 5 HOH A 1 501 19 HOH HOH . H 5 HOH A 2 502 175 HOH HOH . H 5 HOH A 3 503 93 HOH HOH . H 5 HOH A 4 504 18 HOH HOH . H 5 HOH A 5 505 40 HOH HOH . H 5 HOH A 6 506 112 HOH HOH . H 5 HOH A 7 507 123 HOH HOH . H 5 HOH A 8 508 90 HOH HOH . H 5 HOH A 9 509 56 HOH HOH . H 5 HOH A 10 510 11 HOH HOH . H 5 HOH A 11 511 95 HOH HOH . H 5 HOH A 12 512 176 HOH HOH . H 5 HOH A 13 513 118 HOH HOH . H 5 HOH A 14 514 99 HOH HOH . H 5 HOH A 15 515 82 HOH HOH . H 5 HOH A 16 516 130 HOH HOH . H 5 HOH A 17 517 39 HOH HOH . H 5 HOH A 18 518 14 HOH HOH . H 5 HOH A 19 519 79 HOH HOH . H 5 HOH A 20 520 152 HOH HOH . H 5 HOH A 21 521 29 HOH HOH . H 5 HOH A 22 522 119 HOH HOH . H 5 HOH A 23 523 129 HOH HOH . H 5 HOH A 24 524 5 HOH HOH . H 5 HOH A 25 525 37 HOH HOH . H 5 HOH A 26 526 174 HOH HOH . H 5 HOH A 27 527 106 HOH HOH . H 5 HOH A 28 528 35 HOH HOH . H 5 HOH A 29 529 27 HOH HOH . H 5 HOH A 30 530 68 HOH HOH . H 5 HOH A 31 531 136 HOH HOH . H 5 HOH A 32 532 142 HOH HOH . H 5 HOH A 33 533 154 HOH HOH . H 5 HOH A 34 534 145 HOH HOH . H 5 HOH A 35 535 144 HOH HOH . H 5 HOH A 36 536 164 HOH HOH . H 5 HOH A 37 537 126 HOH HOH . H 5 HOH A 38 538 94 HOH HOH . H 5 HOH A 39 539 62 HOH HOH . H 5 HOH A 40 540 92 HOH HOH . H 5 HOH A 41 541 58 HOH HOH . H 5 HOH A 42 542 23 HOH HOH . H 5 HOH A 43 543 105 HOH HOH . H 5 HOH A 44 544 66 HOH HOH . H 5 HOH A 45 545 121 HOH HOH . H 5 HOH A 46 546 108 HOH HOH . H 5 HOH A 47 547 88 HOH HOH . H 5 HOH A 48 548 134 HOH HOH . H 5 HOH A 49 549 148 HOH HOH . H 5 HOH A 50 550 30 HOH HOH . H 5 HOH A 51 551 36 HOH HOH . H 5 HOH A 52 552 49 HOH HOH . H 5 HOH A 53 553 76 HOH HOH . H 5 HOH A 54 554 150 HOH HOH . H 5 HOH A 55 555 158 HOH HOH . H 5 HOH A 56 556 85 HOH HOH . H 5 HOH A 57 557 28 HOH HOH . H 5 HOH A 58 558 165 HOH HOH . H 5 HOH A 59 559 43 HOH HOH . H 5 HOH A 60 560 4 HOH HOH . H 5 HOH A 61 561 131 HOH HOH . H 5 HOH A 62 562 155 HOH HOH . H 5 HOH A 63 563 117 HOH HOH . H 5 HOH A 64 564 77 HOH HOH . H 5 HOH A 65 565 125 HOH HOH . H 5 HOH A 66 566 21 HOH HOH . H 5 HOH A 67 567 137 HOH HOH . H 5 HOH A 68 568 113 HOH HOH . H 5 HOH A 69 569 54 HOH HOH . H 5 HOH A 70 570 1 HOH HOH . H 5 HOH A 71 571 172 HOH HOH . H 5 HOH A 72 572 74 HOH HOH . H 5 HOH A 73 573 42 HOH HOH . H 5 HOH A 74 574 22 HOH HOH . H 5 HOH A 75 575 147 HOH HOH . H 5 HOH A 76 576 151 HOH HOH . H 5 HOH A 77 577 171 HOH HOH . H 5 HOH A 78 578 2 HOH HOH . H 5 HOH A 79 579 67 HOH HOH . H 5 HOH A 80 580 168 HOH HOH . H 5 HOH A 81 581 64 HOH HOH . H 5 HOH A 82 582 31 HOH HOH . H 5 HOH A 83 583 13 HOH HOH . H 5 HOH A 84 584 157 HOH HOH . I 5 HOH B 1 501 32 HOH HOH . I 5 HOH B 2 502 87 HOH HOH . I 5 HOH B 3 503 41 HOH HOH . I 5 HOH B 4 504 120 HOH HOH . I 5 HOH B 5 505 141 HOH HOH . I 5 HOH B 6 506 124 HOH HOH . I 5 HOH B 7 507 91 HOH HOH . I 5 HOH B 8 508 61 HOH HOH . I 5 HOH B 9 509 60 HOH HOH . I 5 HOH B 10 510 140 HOH HOH . I 5 HOH B 11 511 25 HOH HOH . I 5 HOH B 12 512 132 HOH HOH . I 5 HOH B 13 513 46 HOH HOH . I 5 HOH B 14 514 98 HOH HOH . I 5 HOH B 15 515 111 HOH HOH . I 5 HOH B 16 516 97 HOH HOH . I 5 HOH B 17 517 104 HOH HOH . I 5 HOH B 18 518 55 HOH HOH . I 5 HOH B 19 519 110 HOH HOH . I 5 HOH B 20 520 52 HOH HOH . I 5 HOH B 21 521 8 HOH HOH . I 5 HOH B 22 522 72 HOH HOH . I 5 HOH B 23 523 57 HOH HOH . I 5 HOH B 24 524 69 HOH HOH . I 5 HOH B 25 525 143 HOH HOH . I 5 HOH B 26 526 12 HOH HOH . I 5 HOH B 27 527 167 HOH HOH . I 5 HOH B 28 528 127 HOH HOH . I 5 HOH B 29 529 48 HOH HOH . I 5 HOH B 30 530 20 HOH HOH . I 5 HOH B 31 531 65 HOH HOH . I 5 HOH B 32 532 15 HOH HOH . I 5 HOH B 33 533 116 HOH HOH . I 5 HOH B 34 534 17 HOH HOH . I 5 HOH B 35 535 173 HOH HOH . I 5 HOH B 36 536 146 HOH HOH . I 5 HOH B 37 537 7 HOH HOH . I 5 HOH B 38 538 139 HOH HOH . I 5 HOH B 39 539 38 HOH HOH . I 5 HOH B 40 540 83 HOH HOH . I 5 HOH B 41 541 100 HOH HOH . I 5 HOH B 42 542 6 HOH HOH . I 5 HOH B 43 543 169 HOH HOH . I 5 HOH B 44 544 115 HOH HOH . I 5 HOH B 45 545 109 HOH HOH . I 5 HOH B 46 546 89 HOH HOH . I 5 HOH B 47 547 149 HOH HOH . I 5 HOH B 48 548 81 HOH HOH . I 5 HOH B 49 549 59 HOH HOH . I 5 HOH B 50 550 34 HOH HOH . I 5 HOH B 51 551 44 HOH HOH . I 5 HOH B 52 552 47 HOH HOH . I 5 HOH B 53 553 101 HOH HOH . I 5 HOH B 54 554 80 HOH HOH . I 5 HOH B 55 555 24 HOH HOH . I 5 HOH B 56 556 50 HOH HOH . I 5 HOH B 57 557 153 HOH HOH . I 5 HOH B 58 558 162 HOH HOH . I 5 HOH B 59 559 84 HOH HOH . I 5 HOH B 60 560 16 HOH HOH . I 5 HOH B 61 561 45 HOH HOH . I 5 HOH B 62 562 26 HOH HOH . I 5 HOH B 63 563 33 HOH HOH . I 5 HOH B 64 564 102 HOH HOH . I 5 HOH B 65 565 53 HOH HOH . I 5 HOH B 66 566 128 HOH HOH . I 5 HOH B 67 567 107 HOH HOH . I 5 HOH B 68 568 166 HOH HOH . I 5 HOH B 69 569 122 HOH HOH . I 5 HOH B 70 570 70 HOH HOH . I 5 HOH B 71 571 10 HOH HOH . I 5 HOH B 72 572 133 HOH HOH . I 5 HOH B 73 573 3 HOH HOH . I 5 HOH B 74 574 135 HOH HOH . I 5 HOH B 75 575 73 HOH HOH . I 5 HOH B 76 576 103 HOH HOH . I 5 HOH B 77 577 78 HOH HOH . I 5 HOH B 78 578 51 HOH HOH . I 5 HOH B 79 579 9 HOH HOH . I 5 HOH B 80 580 75 HOH HOH . I 5 HOH B 81 581 170 HOH HOH . I 5 HOH B 82 582 63 HOH HOH . I 5 HOH B 83 583 86 HOH HOH . I 5 HOH B 84 584 163 HOH HOH . I 5 HOH B 85 585 156 HOH HOH . I 5 HOH B 86 586 138 HOH HOH . I 5 HOH B 87 587 71 HOH HOH . I 5 HOH B 88 588 159 HOH HOH . I 5 HOH B 89 589 160 HOH HOH . I 5 HOH B 90 590 161 HOH HOH . I 5 HOH B 91 591 96 HOH HOH . I 5 HOH B 92 592 114 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 . . . D 3 35.827 -1.257 19.954 0.8 68.11 ? N1 PLP 402 A 1 HETATM 2 C C2 PLP . . . D 3 34.941 -1.343 18.963 0.8 70.34 ? C2 PLP 402 A 1 HETATM 3 C C2A PLP . . . D 3 34.114 -0.139 18.639 0.8 66.94 ? C2A PLP 402 A 1 HETATM 4 C C3 PLP . . . D 3 34.794 -2.546 18.244 0.8 65.66 ? C3 PLP 402 A 1 HETATM 5 O O3 PLP . . . D 3 33.882 -2.603 17.249 0.8 61.82 ? O3 PLP 402 A 1 HETATM 6 C C4 PLP . . . D 3 35.585 -3.664 18.577 0.8 67.03 ? C4 PLP 402 A 1 HETATM 7 C C4A PLP . . . D 3 35.404 -4.907 17.819 0.8 68.71 ? C4A PLP 402 A 1 HETATM 8 C C5 PLP . . . D 3 36.504 -3.533 19.636 0.8 71.23 ? C5 PLP 402 A 1 HETATM 9 C C6 PLP . . . D 3 36.586 -2.326 20.278 0.8 72.49 ? C6 PLP 402 A 1 HETATM 10 C C5A PLP . . . D 3 37.414 -4.652 20.059 0.8 64.4 ? C5A PLP 402 A 1 HETATM 11 O O4P PLP . . . D 3 36.667 -5.784 20.601 0.8 72.23 ? O4P PLP 402 A 1 HETATM 12 P P PLP . . . D 3 37.247 -7.287 20.462 0.8 67.71 ? P PLP 402 A 1 HETATM 13 O O1P PLP . . . D 3 37.792 -7.386 19.044 0.8 51.56 ? O1P PLP 402 A 1 HETATM 14 O O2P PLP . . . D 3 38.332 -7.418 21.521 0.8 49.99 ? O2P PLP 402 A 1 HETATM 15 O O3P PLP . . . D 3 36.049 -8.202 20.715 0.8 47.92 ? O3P PLP 402 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 44 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #