data_3DXV # _model_server_result.job_id iA2o3e5zUSiqmXS7ogfZLg _model_server_result.datetime_utc '2024-11-28 02:12:33' _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 3dxv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":450}' # _entry.id 3DXV # _exptl.entry_id 3DXV _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 103.22 _cell.angle_gamma 90 _cell.entry_id 3DXV _cell.length_a 56.547 _cell.length_b 61.063 _cell.length_c 105.227 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3DXV _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 ? 2 C N N ? 2 D 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 covale ? covale1 A NZ LYS 270 A LYS 267 1_555 C C4A PLP . A PLP 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale2 B NZ LYS 270 B LYS 267 1_555 D C4A PLP . B PLP 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? # _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 3DXV _atom_sites.fract_transf_matrix[1][1] 0.017684 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004156 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016377 _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] 0.009762 _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 1 450 450 PLP PLP . D 2 PLP B 1 450 450 PLP PLP . E 3 HOH A 1 451 1 HOH HOH . E 3 HOH A 2 452 3 HOH HOH . E 3 HOH A 3 453 4 HOH HOH . E 3 HOH A 4 454 5 HOH HOH . E 3 HOH A 5 455 7 HOH HOH . E 3 HOH A 6 456 10 HOH HOH . E 3 HOH A 7 457 12 HOH HOH . E 3 HOH A 8 458 13 HOH HOH . E 3 HOH A 9 459 15 HOH HOH . E 3 HOH A 10 460 17 HOH HOH . E 3 HOH A 11 461 19 HOH HOH . E 3 HOH A 12 462 20 HOH HOH . E 3 HOH A 13 463 22 HOH HOH . E 3 HOH A 14 464 23 HOH HOH . E 3 HOH A 15 465 24 HOH HOH . E 3 HOH A 16 466 25 HOH HOH . E 3 HOH A 17 467 29 HOH HOH . E 3 HOH A 18 468 31 HOH HOH . E 3 HOH A 19 469 32 HOH HOH . E 3 HOH A 20 470 34 HOH HOH . E 3 HOH A 21 471 36 HOH HOH . E 3 HOH A 22 472 37 HOH HOH . E 3 HOH A 23 473 38 HOH HOH . E 3 HOH A 24 474 41 HOH HOH . E 3 HOH A 25 475 43 HOH HOH . E 3 HOH A 26 476 48 HOH HOH . E 3 HOH A 27 477 50 HOH HOH . E 3 HOH A 28 478 51 HOH HOH . E 3 HOH A 29 479 52 HOH HOH . E 3 HOH A 30 480 53 HOH HOH . E 3 HOH A 31 481 54 HOH HOH . E 3 HOH A 32 482 57 HOH HOH . E 3 HOH A 33 483 62 HOH HOH . E 3 HOH A 34 484 63 HOH HOH . E 3 HOH A 35 485 66 HOH HOH . E 3 HOH A 36 486 67 HOH HOH . E 3 HOH A 37 487 69 HOH HOH . E 3 HOH A 38 488 71 HOH HOH . E 3 HOH A 39 489 72 HOH HOH . E 3 HOH A 40 490 73 HOH HOH . E 3 HOH A 41 491 74 HOH HOH . E 3 HOH A 42 492 75 HOH HOH . E 3 HOH A 43 493 77 HOH HOH . E 3 HOH A 44 494 78 HOH HOH . E 3 HOH A 45 495 79 HOH HOH . E 3 HOH A 46 496 83 HOH HOH . E 3 HOH A 47 497 84 HOH HOH . E 3 HOH A 48 498 85 HOH HOH . E 3 HOH A 49 499 86 HOH HOH . E 3 HOH A 50 500 88 HOH HOH . E 3 HOH A 51 501 89 HOH HOH . E 3 HOH A 52 502 90 HOH HOH . E 3 HOH A 53 503 91 HOH HOH . E 3 HOH A 54 504 92 HOH HOH . E 3 HOH A 55 505 95 HOH HOH . E 3 HOH A 56 506 100 HOH HOH . E 3 HOH A 57 507 103 HOH HOH . E 3 HOH A 58 508 104 HOH HOH . E 3 HOH A 59 509 106 HOH HOH . E 3 HOH A 60 510 109 HOH HOH . E 3 HOH A 61 511 110 HOH HOH . E 3 HOH A 62 512 112 HOH HOH . E 3 HOH A 63 513 115 HOH HOH . E 3 HOH A 64 514 116 HOH HOH . E 3 HOH A 65 515 117 HOH HOH . E 3 HOH A 66 516 119 HOH HOH . F 3 HOH B 1 451 2 HOH HOH . F 3 HOH B 2 452 6 HOH HOH . F 3 HOH B 3 453 8 HOH HOH . F 3 HOH B 4 454 9 HOH HOH . F 3 HOH B 5 455 11 HOH HOH . F 3 HOH B 6 456 14 HOH HOH . F 3 HOH B 7 457 16 HOH HOH . F 3 HOH B 8 458 18 HOH HOH . F 3 HOH B 9 459 21 HOH HOH . F 3 HOH B 10 460 26 HOH HOH . F 3 HOH B 11 461 27 HOH HOH . F 3 HOH B 12 462 28 HOH HOH . F 3 HOH B 13 463 30 HOH HOH . F 3 HOH B 14 464 33 HOH HOH . F 3 HOH B 15 465 35 HOH HOH . F 3 HOH B 16 466 39 HOH HOH . F 3 HOH B 17 467 40 HOH HOH . F 3 HOH B 18 468 42 HOH HOH . F 3 HOH B 19 469 44 HOH HOH . F 3 HOH B 20 470 45 HOH HOH . F 3 HOH B 21 471 46 HOH HOH . F 3 HOH B 22 472 47 HOH HOH . F 3 HOH B 23 473 49 HOH HOH . F 3 HOH B 24 474 55 HOH HOH . F 3 HOH B 25 475 56 HOH HOH . F 3 HOH B 26 476 58 HOH HOH . F 3 HOH B 27 477 59 HOH HOH . F 3 HOH B 28 478 60 HOH HOH . F 3 HOH B 29 479 61 HOH HOH . F 3 HOH B 30 480 64 HOH HOH . F 3 HOH B 31 481 65 HOH HOH . F 3 HOH B 32 482 68 HOH HOH . F 3 HOH B 33 483 70 HOH HOH . F 3 HOH B 34 484 76 HOH HOH . F 3 HOH B 35 485 80 HOH HOH . F 3 HOH B 36 486 81 HOH HOH . F 3 HOH B 37 487 82 HOH HOH . F 3 HOH B 38 488 87 HOH HOH . F 3 HOH B 39 489 93 HOH HOH . F 3 HOH B 40 490 94 HOH HOH . F 3 HOH B 41 491 96 HOH HOH . F 3 HOH B 42 492 97 HOH HOH . F 3 HOH B 43 493 98 HOH HOH . F 3 HOH B 44 494 99 HOH HOH . F 3 HOH B 45 495 101 HOH HOH . F 3 HOH B 46 496 102 HOH HOH . F 3 HOH B 47 497 105 HOH HOH . F 3 HOH B 48 498 107 HOH HOH . F 3 HOH B 49 499 108 HOH HOH . F 3 HOH B 50 500 111 HOH HOH . F 3 HOH B 51 501 113 HOH HOH . F 3 HOH B 52 502 114 HOH HOH . F 3 HOH B 53 503 118 HOH HOH . F 3 HOH B 54 504 120 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 2 16.134 -19.574 16.816 1 23.27 ? N1 PLP 450 B 1 HETATM 2 C C2 PLP . . . D 2 17.408 -19.947 16.445 1 23.34 ? C2 PLP 450 B 1 HETATM 3 C C2A PLP . . . D 2 17.629 -20.745 15.187 1 23.57 ? C2A PLP 450 B 1 HETATM 4 C C3 PLP . . . D 2 18.484 -19.576 17.241 1 24.16 ? C3 PLP 450 B 1 HETATM 5 O O3 PLP . . . D 2 19.614 -19.907 16.894 1 24.72 ? O3 PLP 450 B 1 HETATM 6 C C4 PLP . . . D 2 18.295 -18.827 18.413 1 24.55 ? C4 PLP 450 B 1 HETATM 7 C C4A PLP . . . D 2 19.501 -18.432 19.243 1 24.54 ? C4A PLP 450 B 1 HETATM 8 C C5 PLP . . . D 2 16.988 -18.472 18.781 1 23.39 ? C5 PLP 450 B 1 HETATM 9 C C6 PLP . . . D 2 15.921 -18.852 17.972 1 23.58 ? C6 PLP 450 B 1 HETATM 10 C C5A PLP . . . D 2 16.693 -17.682 20.021 1 22.07 ? C5A PLP 450 B 1 HETATM 11 O O4P PLP . . . D 2 17.366 -16.418 20.209 1 19.89 ? O4P PLP 450 B 1 HETATM 12 P P PLP . . . D 2 17.574 -15.844 21.688 1 17.71 ? P PLP 450 B 1 HETATM 13 O O1P PLP . . . D 2 16.193 -15.545 22.151 1 17.38 ? O1P PLP 450 B 1 HETATM 14 O O2P PLP . . . D 2 18.205 -16.983 22.399 1 18.86 ? O2P PLP 450 B 1 HETATM 15 O O3P PLP . . . D 2 18.452 -14.673 21.518 1 18.95 ? O3P PLP 450 B 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #