data_6ZVG # _model_server_result.job_id Nf1qnu9tFhpaBfn4ai6FnA _model_server_result.datetime_utc '2024-11-28 22:19:41' _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 6zvg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":404}' # _entry.id 6ZVG # _exptl.entry_id 6ZVG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 4 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 106.42 _cell.angle_gamma 90 _cell.entry_id 6ZVG _cell.length_a 177.267 _cell.length_b 82.286 _cell.length_c 98.208 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6ZVG _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,I,J,K,P,Q 1 1 C,D,L,M,N,O,R,S 2 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 ? 4 H N N ? 4 K N N ? 4 M N N ? 4 O 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 246 A LYS 246 1_555 H C4A PLP . A PLP 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? covale ? covale2 B NZ LYS 246 B LYS 246 1_555 K C4A PLP . B PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.271 ? covale ? covale3 C NZ LYS 246 C LYS 246 1_555 M C4A PLP . C PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.284 ? covale ? covale4 D NZ LYS 246 D LYS 246 1_555 O C4A PLP . D PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.265 ? metalc ? metalc1 E MG MG . A MG 401 1_555 G O3 NO3 . A NO3 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? metalc ? metalc2 E MG MG . A MG 401 1_555 P O HOH . A HOH 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc3 E MG MG . A MG 401 1_555 R O HOH . C HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc4 F MG MG . A MG 402 1_555 P O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc5 F MG MG . A MG 402 1_555 P O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 F MG MG . A MG 402 1_555 Q O HOH . B HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc7 F MG MG . A MG 402 1_555 Q O HOH . B HOH 524 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc8 L MG MG . C MG 401 1_555 R O HOH . C HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc9 L MG MG . C MG 401 1_555 R O HOH . C HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc10 L MG MG . C MG 401 1_555 S O HOH . D HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc11 L MG MG . C MG 401 1_555 S O HOH . D HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? # _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 290 n y N1 C6 PLP sing 291 n y C2 C2A PLP sing 292 n n C2 C3 PLP sing 293 n y C2A H2A1 PLP sing 294 n n C2A H2A2 PLP sing 295 n n C2A H2A3 PLP sing 296 n n C3 O3 PLP sing 297 n n C3 C4 PLP doub 298 n y O3 HO3 PLP sing 299 n n C4 C4A PLP sing 300 n n C4 C5 PLP sing 301 n y C4A O4A PLP doub 302 n n C4A H4A PLP sing 303 n n C5 C6 PLP doub 304 n y C5 C5A PLP sing 305 n n C6 H6 PLP sing 306 n n C5A O4P PLP sing 307 n n C5A H5A1 PLP sing 308 n n C5A H5A2 PLP sing 309 n n O4P P PLP sing 310 n n P O1P PLP doub 311 n n P O2P PLP sing 312 n n P O3P PLP sing 313 n n O2P HOP2 PLP sing 314 n n O3P HOP3 PLP sing 315 n n # _atom_sites.entry_id 6ZVG _atom_sites.fract_transf_matrix[1][1] 0.005641 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001662 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012153 _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] 0.010615 _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 E 2 MG A 1 401 1 MG MG . F 2 MG A 1 402 2 MG MG . G 3 NO3 A 1 403 1 NO3 NO3 . H 4 PLP A 1 404 1 PLP PLP . I 5 3IL A 1 405 1 3IL 3IL . J 3 NO3 B 1 401 2 NO3 NO3 . K 4 PLP B 1 402 2 PLP PLP . L 2 MG C 1 401 3 MG MG . M 4 PLP C 1 402 3 PLP PLP . N 5 3IL C 1 403 2 3IL 3IL . O 4 PLP D 1 401 4 PLP PLP . P 6 HOH A 1 501 32 HOH HOH . P 6 HOH A 2 502 150 HOH HOH . P 6 HOH A 3 503 1 HOH HOH . P 6 HOH A 4 504 46 HOH HOH . P 6 HOH A 5 505 117 HOH HOH . P 6 HOH A 6 506 75 HOH HOH . P 6 HOH A 7 507 8 HOH HOH . P 6 HOH A 8 508 19 HOH HOH . P 6 HOH A 9 509 100 HOH HOH . P 6 HOH A 10 510 39 HOH HOH . P 6 HOH A 11 511 61 HOH HOH . P 6 HOH A 12 512 48 HOH HOH . P 6 HOH A 13 513 47 HOH HOH . P 6 HOH A 14 514 41 HOH HOH . P 6 HOH A 15 515 87 HOH HOH . P 6 HOH A 16 516 40 HOH HOH . P 6 HOH A 17 517 38 HOH HOH . P 6 HOH A 18 518 113 HOH HOH . P 6 HOH A 19 519 6 HOH HOH . P 6 HOH A 20 520 4 HOH HOH . P 6 HOH A 21 521 16 HOH HOH . P 6 HOH A 22 522 153 HOH HOH . P 6 HOH A 23 523 91 HOH HOH . P 6 HOH A 24 524 71 HOH HOH . P 6 HOH A 25 525 144 HOH HOH . P 6 HOH A 26 526 108 HOH HOH . P 6 HOH A 27 527 106 HOH HOH . P 6 HOH A 28 528 121 HOH HOH . P 6 HOH A 29 529 2 HOH HOH . P 6 HOH A 30 530 122 HOH HOH . P 6 HOH A 31 531 95 HOH HOH . P 6 HOH A 32 532 83 HOH HOH . P 6 HOH A 33 533 30 HOH HOH . P 6 HOH A 34 534 90 HOH HOH . P 6 HOH A 35 535 138 HOH HOH . P 6 HOH A 36 536 120 HOH HOH . P 6 HOH A 37 537 88 HOH HOH . P 6 HOH A 38 538 114 HOH HOH . P 6 HOH A 39 539 97 HOH HOH . P 6 HOH A 40 540 94 HOH HOH . P 6 HOH A 41 541 86 HOH HOH . P 6 HOH A 42 542 102 HOH HOH . P 6 HOH A 43 543 112 HOH HOH . P 6 HOH A 44 544 85 HOH HOH . P 6 HOH A 45 545 151 HOH HOH . P 6 HOH A 46 546 89 HOH HOH . Q 6 HOH B 1 501 69 HOH HOH . Q 6 HOH B 2 502 7 HOH HOH . Q 6 HOH B 3 503 56 HOH HOH . Q 6 HOH B 4 504 55 HOH HOH . Q 6 HOH B 5 505 3 HOH HOH . Q 6 HOH B 6 506 76 HOH HOH . Q 6 HOH B 7 507 111 HOH HOH . Q 6 HOH B 8 508 92 HOH HOH . Q 6 HOH B 9 509 34 HOH HOH . Q 6 HOH B 10 510 33 HOH HOH . Q 6 HOH B 11 511 9 HOH HOH . Q 6 HOH B 12 512 146 HOH HOH . Q 6 HOH B 13 513 78 HOH HOH . Q 6 HOH B 14 514 36 HOH HOH . Q 6 HOH B 15 515 81 HOH HOH . Q 6 HOH B 16 516 35 HOH HOH . Q 6 HOH B 17 517 37 HOH HOH . Q 6 HOH B 18 518 50 HOH HOH . Q 6 HOH B 19 519 12 HOH HOH . Q 6 HOH B 20 520 107 HOH HOH . Q 6 HOH B 21 521 14 HOH HOH . Q 6 HOH B 22 522 98 HOH HOH . Q 6 HOH B 23 523 125 HOH HOH . Q 6 HOH B 24 524 105 HOH HOH . Q 6 HOH B 25 525 118 HOH HOH . Q 6 HOH B 26 526 58 HOH HOH . Q 6 HOH B 27 527 44 HOH HOH . Q 6 HOH B 28 528 135 HOH HOH . Q 6 HOH B 29 529 67 HOH HOH . Q 6 HOH B 30 530 43 HOH HOH . Q 6 HOH B 31 531 160 HOH HOH . Q 6 HOH B 32 532 124 HOH HOH . Q 6 HOH B 33 533 13 HOH HOH . Q 6 HOH B 34 534 57 HOH HOH . Q 6 HOH B 35 535 154 HOH HOH . Q 6 HOH B 36 536 116 HOH HOH . Q 6 HOH B 37 537 136 HOH HOH . R 6 HOH C 1 501 10 HOH HOH . R 6 HOH C 2 502 127 HOH HOH . R 6 HOH C 3 503 77 HOH HOH . R 6 HOH C 4 504 11 HOH HOH . R 6 HOH C 5 505 128 HOH HOH . R 6 HOH C 6 506 49 HOH HOH . R 6 HOH C 7 507 96 HOH HOH . R 6 HOH C 8 508 141 HOH HOH . R 6 HOH C 9 509 31 HOH HOH . R 6 HOH C 10 510 103 HOH HOH . R 6 HOH C 11 511 74 HOH HOH . R 6 HOH C 12 512 119 HOH HOH . R 6 HOH C 13 513 73 HOH HOH . R 6 HOH C 14 514 52 HOH HOH . R 6 HOH C 15 515 115 HOH HOH . R 6 HOH C 16 516 145 HOH HOH . R 6 HOH C 17 517 104 HOH HOH . R 6 HOH C 18 518 137 HOH HOH . R 6 HOH C 19 519 5 HOH HOH . R 6 HOH C 20 520 163 HOH HOH . R 6 HOH C 21 521 123 HOH HOH . R 6 HOH C 22 522 126 HOH HOH . R 6 HOH C 23 523 64 HOH HOH . R 6 HOH C 24 524 62 HOH HOH . R 6 HOH C 25 525 152 HOH HOH . R 6 HOH C 26 526 22 HOH HOH . R 6 HOH C 27 527 131 HOH HOH . R 6 HOH C 28 528 45 HOH HOH . R 6 HOH C 29 529 60 HOH HOH . R 6 HOH C 30 530 84 HOH HOH . R 6 HOH C 31 531 70 HOH HOH . R 6 HOH C 32 532 129 HOH HOH . R 6 HOH C 33 533 142 HOH HOH . R 6 HOH C 34 534 65 HOH HOH . R 6 HOH C 35 535 148 HOH HOH . R 6 HOH C 36 536 149 HOH HOH . R 6 HOH C 37 537 143 HOH HOH . R 6 HOH C 38 538 63 HOH HOH . R 6 HOH C 39 539 139 HOH HOH . S 6 HOH D 1 501 54 HOH HOH . S 6 HOH D 2 502 42 HOH HOH . S 6 HOH D 3 503 68 HOH HOH . S 6 HOH D 4 504 27 HOH HOH . S 6 HOH D 5 505 80 HOH HOH . S 6 HOH D 6 506 18 HOH HOH . S 6 HOH D 7 507 25 HOH HOH . S 6 HOH D 8 508 162 HOH HOH . S 6 HOH D 9 509 51 HOH HOH . S 6 HOH D 10 510 17 HOH HOH . S 6 HOH D 11 511 147 HOH HOH . S 6 HOH D 12 512 20 HOH HOH . S 6 HOH D 13 513 99 HOH HOH . S 6 HOH D 14 514 59 HOH HOH . S 6 HOH D 15 515 159 HOH HOH . S 6 HOH D 16 516 66 HOH HOH . S 6 HOH D 17 517 101 HOH HOH . S 6 HOH D 18 518 157 HOH HOH . S 6 HOH D 19 519 28 HOH HOH . S 6 HOH D 20 520 23 HOH HOH . S 6 HOH D 21 521 79 HOH HOH . S 6 HOH D 22 522 130 HOH HOH . S 6 HOH D 23 523 133 HOH HOH . S 6 HOH D 24 524 158 HOH HOH . S 6 HOH D 25 525 140 HOH HOH . S 6 HOH D 26 526 109 HOH HOH . S 6 HOH D 27 527 82 HOH HOH . S 6 HOH D 28 528 110 HOH HOH . S 6 HOH D 29 529 21 HOH HOH . S 6 HOH D 30 530 15 HOH HOH . S 6 HOH D 31 531 26 HOH HOH . S 6 HOH D 32 532 155 HOH HOH . S 6 HOH D 33 533 132 HOH HOH . S 6 HOH D 34 534 156 HOH HOH . S 6 HOH D 35 535 161 HOH HOH . S 6 HOH D 36 536 24 HOH HOH . S 6 HOH D 37 537 53 HOH HOH . S 6 HOH D 38 538 29 HOH HOH . S 6 HOH D 39 539 93 HOH HOH . S 6 HOH D 40 540 134 HOH HOH . S 6 HOH D 41 541 72 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 . . . H 4 54.967 27.267 64.924 1 59.78 ? N1 PLP 404 A 1 HETATM 2 C C2 PLP . . . H 4 55.186 26.186 65.725 1 59.47 ? C2 PLP 404 A 1 HETATM 3 C C2A PLP . . . H 4 55.904 24.983 65.163 1 62.5 ? C2A PLP 404 A 1 HETATM 4 C C3 PLP . . . H 4 54.751 26.189 67.055 1 59.98 ? C3 PLP 404 A 1 HETATM 5 O O3 PLP . . . H 4 54.98 25.086 67.858 1 55.36 ? O3 PLP 404 A 1 HETATM 6 C C4 PLP . . . H 4 54.096 27.281 67.572 1 61.18 ? C4 PLP 404 A 1 HETATM 7 C C4A PLP . . . H 4 53.631 27.277 69.029 1 60.45 ? C4A PLP 404 A 1 HETATM 8 C C5 PLP . . . H 4 53.874 28.393 66.759 1 59.92 ? C5 PLP 404 A 1 HETATM 9 C C6 PLP . . . H 4 54.315 28.356 65.444 1 59.11 ? C6 PLP 404 A 1 HETATM 10 C C5A PLP . . . H 4 53.145 29.614 67.289 1 62.38 ? C5A PLP 404 A 1 HETATM 11 O O4P PLP . . . H 4 54.086 30.612 67.731 1 59.84 ? O4P PLP 404 A 1 HETATM 12 P P PLP . . . H 4 53.45 31.992 68.328 1 56.13 ? P PLP 404 A 1 HETATM 13 O O1P PLP . . . H 4 52.69 32.727 67.234 1 54.71 ? O1P PLP 404 A 1 HETATM 14 O O2P PLP . . . H 4 54.567 32.867 68.894 1 56.27 ? O2P PLP 404 A 1 HETATM 15 O O3P PLP . . . H 4 52.482 31.592 69.427 1 54.87 ? O3P PLP 404 A 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #