data_1VFH # _model_server_result.job_id csgHxD-cmrJwfzhqIrnklg _model_server_result.datetime_utc '2024-11-28 18:08:33' _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 1vfh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 1VFH # _exptl.entry_id 1VFH _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 120.14 _cell.angle_gamma 90 _cell.entry_id 1VFH _cell.length_a 83.98 _cell.length_b 63.38 _cell.length_c 85.95 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VFH _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _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 _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' 2_556 -x,y,-z+1 -1 0 0 0 1 0 0 0 -1 -43.15675 0 74.329654 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 covale ? covale1 A NZ LYS 38 A LYS 38 1_555 B C4A PLP . A PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.494 ? covale ? covale2 A C LEU 128 A LEU 128 1_555 A N KCX 129 A KCX 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale3 A C KCX 129 A KCX 129 1_555 A N ALA 130 A ALA 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? # _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 286 n y N1 C6 PLP sing 287 n y C2 C2A PLP sing 288 n n C2 C3 PLP sing 289 n y C2A H2A1 PLP sing 290 n n C2A H2A2 PLP sing 291 n n C2A H2A3 PLP sing 292 n n C3 O3 PLP sing 293 n n C3 C4 PLP doub 294 n y O3 HO3 PLP sing 295 n n C4 C4A PLP sing 296 n n C4 C5 PLP sing 297 n y C4A O4A PLP doub 298 n n C4A H4A PLP sing 299 n n C5 C6 PLP doub 300 n y C5 C5A PLP sing 301 n n C6 H6 PLP sing 302 n n C5A O4P PLP sing 303 n n C5A H5A1 PLP sing 304 n n C5A H5A2 PLP sing 305 n n O4P P PLP sing 306 n n P O1P PLP doub 307 n n P O2P PLP sing 308 n n P O3P PLP sing 309 n n O2P HOP2 PLP sing 310 n n O3P HOP3 PLP sing 311 n n # _atom_sites.entry_id 1VFH _atom_sites.fract_transf_matrix[1][1] 0.011908 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006914 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015778 _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] 0.013454 _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 PLP A 1 401 401 PLP PLP . C 3 HOH A 1 501 501 HOH HOH . C 3 HOH A 2 502 502 HOH HOH . C 3 HOH A 3 503 503 HOH HOH . C 3 HOH A 4 504 504 HOH HOH . C 3 HOH A 5 505 505 HOH HOH . C 3 HOH A 6 506 506 HOH HOH . C 3 HOH A 7 507 507 HOH HOH . C 3 HOH A 8 508 508 HOH HOH . C 3 HOH A 9 509 509 HOH HOH . C 3 HOH A 10 510 510 HOH HOH . C 3 HOH A 11 511 511 HOH HOH . C 3 HOH A 12 512 512 HOH HOH . C 3 HOH A 13 513 513 HOH HOH . C 3 HOH A 14 514 514 HOH HOH . C 3 HOH A 15 515 515 HOH HOH . C 3 HOH A 16 516 516 HOH HOH . C 3 HOH A 17 517 517 HOH HOH . C 3 HOH A 18 518 518 HOH HOH . C 3 HOH A 19 519 519 HOH HOH . C 3 HOH A 20 520 520 HOH HOH . C 3 HOH A 21 521 521 HOH HOH . C 3 HOH A 22 522 522 HOH HOH . C 3 HOH A 23 523 523 HOH HOH . C 3 HOH A 24 524 524 HOH HOH . C 3 HOH A 25 525 525 HOH HOH . C 3 HOH A 26 526 526 HOH HOH . C 3 HOH A 27 527 527 HOH HOH . C 3 HOH A 28 528 528 HOH HOH . C 3 HOH A 29 529 529 HOH HOH . C 3 HOH A 30 530 530 HOH HOH . C 3 HOH A 31 531 531 HOH HOH . C 3 HOH A 32 532 532 HOH HOH . C 3 HOH A 33 533 533 HOH HOH . C 3 HOH A 34 534 534 HOH HOH . C 3 HOH A 35 535 535 HOH HOH . C 3 HOH A 36 536 536 HOH HOH . C 3 HOH A 37 537 537 HOH HOH . C 3 HOH A 38 538 538 HOH HOH . C 3 HOH A 39 539 539 HOH HOH . C 3 HOH A 40 540 540 HOH HOH . C 3 HOH A 41 541 541 HOH HOH . C 3 HOH A 42 542 542 HOH HOH . C 3 HOH A 43 543 543 HOH HOH . C 3 HOH A 44 544 544 HOH HOH . C 3 HOH A 45 545 545 HOH HOH . C 3 HOH A 46 546 546 HOH HOH . C 3 HOH A 47 547 547 HOH HOH . C 3 HOH A 48 548 548 HOH HOH . C 3 HOH A 49 549 549 HOH HOH . C 3 HOH A 50 550 550 HOH HOH . C 3 HOH A 51 551 551 HOH HOH . C 3 HOH A 52 552 552 HOH HOH . C 3 HOH A 53 553 553 HOH HOH . C 3 HOH A 54 554 554 HOH HOH . C 3 HOH A 55 555 555 HOH HOH . C 3 HOH A 56 556 556 HOH HOH . C 3 HOH A 57 557 557 HOH HOH . C 3 HOH A 58 558 558 HOH HOH . C 3 HOH A 59 559 559 HOH HOH . C 3 HOH A 60 560 560 HOH HOH . C 3 HOH A 61 561 561 HOH HOH . C 3 HOH A 62 562 562 HOH HOH . C 3 HOH A 63 563 563 HOH HOH . C 3 HOH A 64 564 564 HOH HOH . C 3 HOH A 65 565 565 HOH HOH . C 3 HOH A 66 566 566 HOH HOH . C 3 HOH A 67 567 567 HOH HOH . C 3 HOH A 68 568 568 HOH HOH . C 3 HOH A 69 569 569 HOH HOH . C 3 HOH A 70 570 570 HOH HOH . C 3 HOH A 71 571 571 HOH HOH . C 3 HOH A 72 572 572 HOH HOH . C 3 HOH A 73 573 573 HOH HOH . C 3 HOH A 74 574 574 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 . . . B 2 -12.622 -1.541 17.977 1 16.63 ? N1 PLP 401 A 1 HETATM 2 C C2 PLP . . . B 2 -13.991 -1.488 18.273 1 17.18 ? C2 PLP 401 A 1 HETATM 3 C C2A PLP . . . B 2 -15.03 -1.453 17.179 1 14.91 ? C2A PLP 401 A 1 HETATM 4 C C3 PLP . . . B 2 -14.353 -1.471 19.598 1 18.39 ? C3 PLP 401 A 1 HETATM 5 O O3 PLP . . . B 2 -15.647 -1.435 19.964 1 20.88 ? O3 PLP 401 A 1 HETATM 6 C C4 PLP . . . B 2 -13.339 -1.503 20.588 1 15.97 ? C4 PLP 401 A 1 HETATM 7 C C4A PLP . . . B 2 -13.741 -1.325 22.117 1 10.99 ? C4A PLP 401 A 1 HETATM 8 C C5 PLP . . . B 2 -11.973 -1.57 20.197 1 20.31 ? C5 PLP 401 A 1 HETATM 9 C C6 PLP . . . B 2 -11.65 -1.583 18.912 1 22.19 ? C6 PLP 401 A 1 HETATM 10 C C5A PLP . . . B 2 -10.845 -1.686 21.211 1 18.35 ? C5A PLP 401 A 1 HETATM 11 O O4P PLP . . . B 2 -10.768 -3.03 21.698 1 18.69 ? O4P PLP 401 A 1 HETATM 12 P P PLP . . . B 2 -9.705 -3.538 22.759 1 18.56 ? P PLP 401 A 1 HETATM 13 O O1P PLP . . . B 2 -8.415 -2.999 22.332 1 20.47 ? O1P PLP 401 A 1 HETATM 14 O O2P PLP . . . B 2 -10.123 -3.004 24.052 1 22.65 ? O2P PLP 401 A 1 HETATM 15 O O3P PLP . . . B 2 -9.74 -4.994 22.74 1 13.82 ? O3P PLP 401 A 1 # _model_server_stats.io_time_ms 81 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #