data_3VSD # _model_server_result.job_id mdUNEDxw-LZWRtltKKYOhw _model_server_result.datetime_utc '2025-02-27 01:26:34' _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 3vsd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 3VSD # _exptl.entry_id 3VSD _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 3VSD _cell.length_a 75.646 _cell.length_b 75.646 _cell.length_c 275.784 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VSD _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,H 1 1 B,F,G,I 2 1 A,B,C,D,E,F,G,H,I 3 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 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 36 A CYS 36 1_555 A SG CYS 64 A CYS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf2 B SG CYS 36 B CYS 36 1_555 B SG CYS 64 B CYS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? covale ? covale1 C C4A PLP . A PLP 401 1_555 D N OAS . A OAS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.739 ? covale ? covale2 F C4A PLP . B PLP 401 1_555 G N OAS . B OAS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.794 ? # _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' # _atom_sites.entry_id 3VSD _atom_sites.fract_transf_matrix[1][1] 0.013219 _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] 0.013219 _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] 0.003626 _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 1 401 400 PLP PLP . D 3 OAS A 1 402 5765 OAS OAS . E 4 MPD A 1 403 1 MPD MPD . F 2 PLP B 1 401 400 PLP PLP . G 3 OAS B 1 402 5765 OAS OAS . H 5 HOH A 1 501 2 HOH HOH . H 5 HOH A 2 502 3 HOH HOH . H 5 HOH A 3 503 10 HOH HOH . H 5 HOH A 4 504 13 HOH HOH . H 5 HOH A 5 505 16 HOH HOH . H 5 HOH A 6 506 17 HOH HOH . H 5 HOH A 7 507 22 HOH HOH . H 5 HOH A 8 508 23 HOH HOH . H 5 HOH A 9 509 25 HOH HOH . H 5 HOH A 10 510 26 HOH HOH . H 5 HOH A 11 511 27 HOH HOH . H 5 HOH A 12 512 29 HOH HOH . H 5 HOH A 13 513 31 HOH HOH . H 5 HOH A 14 514 33 HOH HOH . H 5 HOH A 15 515 34 HOH HOH . H 5 HOH A 16 516 36 HOH HOH . H 5 HOH A 17 517 37 HOH HOH . H 5 HOH A 18 518 39 HOH HOH . H 5 HOH A 19 519 40 HOH HOH . H 5 HOH A 20 520 41 HOH HOH . H 5 HOH A 21 521 44 HOH HOH . H 5 HOH A 22 522 45 HOH HOH . H 5 HOH A 23 523 47 HOH HOH . H 5 HOH A 24 524 48 HOH HOH . H 5 HOH A 25 525 49 HOH HOH . H 5 HOH A 26 526 51 HOH HOH . H 5 HOH A 27 527 53 HOH HOH . H 5 HOH A 28 528 55 HOH HOH . H 5 HOH A 29 529 56 HOH HOH . H 5 HOH A 30 530 57 HOH HOH . H 5 HOH A 31 531 59 HOH HOH . H 5 HOH A 32 532 60 HOH HOH . H 5 HOH A 33 533 61 HOH HOH . H 5 HOH A 34 534 65 HOH HOH . H 5 HOH A 35 535 69 HOH HOH . H 5 HOH A 36 536 70 HOH HOH . H 5 HOH A 37 537 71 HOH HOH . H 5 HOH A 38 538 74 HOH HOH . H 5 HOH A 39 539 75 HOH HOH . H 5 HOH A 40 540 78 HOH HOH . H 5 HOH A 41 541 80 HOH HOH . H 5 HOH A 42 542 83 HOH HOH . H 5 HOH A 43 543 84 HOH HOH . H 5 HOH A 44 544 86 HOH HOH . H 5 HOH A 45 545 88 HOH HOH . H 5 HOH A 46 546 90 HOH HOH . H 5 HOH A 47 547 96 HOH HOH . H 5 HOH A 48 548 97 HOH HOH . H 5 HOH A 49 549 99 HOH HOH . I 5 HOH B 1 501 1 HOH HOH . I 5 HOH B 2 502 4 HOH HOH . I 5 HOH B 3 503 5 HOH HOH . I 5 HOH B 4 504 6 HOH HOH . I 5 HOH B 5 505 7 HOH HOH . I 5 HOH B 6 506 8 HOH HOH . I 5 HOH B 7 507 9 HOH HOH . I 5 HOH B 8 508 11 HOH HOH . I 5 HOH B 9 509 12 HOH HOH . I 5 HOH B 10 510 14 HOH HOH . I 5 HOH B 11 511 15 HOH HOH . I 5 HOH B 12 512 18 HOH HOH . I 5 HOH B 13 513 19 HOH HOH . I 5 HOH B 14 514 20 HOH HOH . I 5 HOH B 15 515 21 HOH HOH . I 5 HOH B 16 516 24 HOH HOH . I 5 HOH B 17 517 28 HOH HOH . I 5 HOH B 18 518 30 HOH HOH . I 5 HOH B 19 519 32 HOH HOH . I 5 HOH B 20 520 35 HOH HOH . I 5 HOH B 21 521 38 HOH HOH . I 5 HOH B 22 522 42 HOH HOH . I 5 HOH B 23 523 43 HOH HOH . I 5 HOH B 24 524 46 HOH HOH . I 5 HOH B 25 525 50 HOH HOH . I 5 HOH B 26 526 52 HOH HOH . I 5 HOH B 27 527 54 HOH HOH . I 5 HOH B 28 528 58 HOH HOH . I 5 HOH B 29 529 62 HOH HOH . I 5 HOH B 30 530 63 HOH HOH . I 5 HOH B 31 531 64 HOH HOH . I 5 HOH B 32 532 66 HOH HOH . I 5 HOH B 33 533 67 HOH HOH . I 5 HOH B 34 534 68 HOH HOH . I 5 HOH B 35 535 72 HOH HOH . I 5 HOH B 36 536 73 HOH HOH . I 5 HOH B 37 537 76 HOH HOH . I 5 HOH B 38 538 77 HOH HOH . I 5 HOH B 39 539 79 HOH HOH . I 5 HOH B 40 540 81 HOH HOH . I 5 HOH B 41 541 82 HOH HOH . I 5 HOH B 42 542 85 HOH HOH . I 5 HOH B 43 543 87 HOH HOH . I 5 HOH B 44 544 89 HOH HOH . I 5 HOH B 45 545 91 HOH HOH . I 5 HOH B 46 546 92 HOH HOH . I 5 HOH B 47 547 93 HOH HOH . I 5 HOH B 48 548 94 HOH HOH . I 5 HOH B 49 549 95 HOH HOH . I 5 HOH B 50 550 98 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 . . . F 2 28.435 -2.286 26.196 1 42.52 ? N1 PLP 401 B 1 HETATM 2 C C2 PLP . . . F 2 29.73 -2.646 26.141 1 41.4 ? C2 PLP 401 B 1 HETATM 3 C C2A PLP . . . F 2 30.241 -3.361 24.875 1 35.27 ? C2A PLP 401 B 1 HETATM 4 C C3 PLP . . . F 2 30.557 -2.333 27.208 1 40.12 ? C3 PLP 401 B 1 HETATM 5 O O3 PLP . . . F 2 31.876 -2.674 27.164 1 37.81 ? O3 PLP 401 B 1 HETATM 6 C C4 PLP . . . F 2 29.99 -1.675 28.317 1 41.78 ? C4 PLP 401 B 1 HETATM 7 C C4A PLP . . . F 2 30.804 -1.271 29.535 1 40.15 ? C4A PLP 401 B 1 HETATM 8 C C5 PLP . . . F 2 28.652 -1.341 28.329 1 40.58 ? C5 PLP 401 B 1 HETATM 9 C C6 PLP . . . F 2 27.899 -1.658 27.224 1 39.55 ? C6 PLP 401 B 1 HETATM 10 C C5A PLP . . . F 2 27.94 -0.636 29.468 1 40.63 ? C5A PLP 401 B 1 HETATM 11 O O4P PLP . . . F 2 28.559 0.597 29.849 1 35.65 ? O4P PLP 401 B 1 HETATM 12 P P PLP . . . F 2 28.435 1.004 31.436 1 35.1 ? P PLP 401 B 1 HETATM 13 O O1P PLP . . . F 2 27.234 0.484 32.093 1 26.62 ? O1P PLP 401 B 1 HETATM 14 O O2P PLP . . . F 2 28.398 2.687 31.576 1 32.01 ? O2P PLP 401 B 1 HETATM 15 O O3P PLP . . . F 2 29.789 0.483 31.948 1 29.74 ? O3P PLP 401 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #