data_3VBE # _model_server_result.job_id ezTTomZQUog-5Z2eegEdYg _model_server_result.datetime_utc '2024-11-28 16:40:45' _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 3vbe # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":501}' # _entry.id 3VBE # _exptl.entry_id 3VBE _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 101.89 _cell.angle_gamma 90 _cell.entry_id 3VBE _cell.length_a 190.323 _cell.length_b 154.58 _cell.length_c 70.8 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VBE _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_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,I,J 1 1 C,D,G,H,K,L 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H 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 66 A LYS 95 1_555 E C4A PLP . A PLP 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 ? covale ? covale2 B NZ LYS 66 B LYS 95 1_555 F C4A PLP . B PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale3 C NZ LYS 66 C LYS 95 1_555 G C4A PLP . C PLP 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.138 ? covale ? covale4 D NZ LYS 66 D LYS 95 1_555 H C4A PLP . D PLP 401 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' # _atom_sites.entry_id 3VBE _atom_sites.fract_transf_matrix[1][1] 0.005254 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001106 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006469 _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] 0.014434 _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 PLP A 1 500 500 PLP PLP . F 2 PLP B 1 501 501 PLP PLP . G 2 PLP C 1 401 502 PLP PLP . H 2 PLP D 1 401 503 PLP PLP . I 3 HOH A 1 601 4 HOH HOH . I 3 HOH A 2 602 6 HOH HOH . I 3 HOH A 3 603 9 HOH HOH . I 3 HOH A 4 604 12 HOH HOH . I 3 HOH A 5 605 16 HOH HOH . I 3 HOH A 6 606 25 HOH HOH . I 3 HOH A 7 607 29 HOH HOH . I 3 HOH A 8 608 30 HOH HOH . I 3 HOH A 9 609 35 HOH HOH . I 3 HOH A 10 610 37 HOH HOH . I 3 HOH A 11 611 45 HOH HOH . I 3 HOH A 12 612 48 HOH HOH . I 3 HOH A 13 613 53 HOH HOH . I 3 HOH A 14 614 60 HOH HOH . I 3 HOH A 15 615 61 HOH HOH . I 3 HOH A 16 616 63 HOH HOH . I 3 HOH A 17 617 66 HOH HOH . I 3 HOH A 18 618 67 HOH HOH . I 3 HOH A 19 619 68 HOH HOH . I 3 HOH A 20 620 69 HOH HOH . I 3 HOH A 21 621 72 HOH HOH . I 3 HOH A 22 622 79 HOH HOH . I 3 HOH A 23 623 84 HOH HOH . I 3 HOH A 24 624 91 HOH HOH . I 3 HOH A 25 625 101 HOH HOH . I 3 HOH A 26 626 104 HOH HOH . I 3 HOH A 27 627 110 HOH HOH . I 3 HOH A 28 628 111 HOH HOH . I 3 HOH A 29 629 114 HOH HOH . I 3 HOH A 30 630 116 HOH HOH . I 3 HOH A 31 631 117 HOH HOH . I 3 HOH A 32 632 121 HOH HOH . I 3 HOH A 33 633 122 HOH HOH . I 3 HOH A 34 634 128 HOH HOH . I 3 HOH A 35 635 133 HOH HOH . I 3 HOH A 36 636 134 HOH HOH . I 3 HOH A 37 637 135 HOH HOH . I 3 HOH A 38 638 140 HOH HOH . I 3 HOH A 39 639 143 HOH HOH . I 3 HOH A 40 640 145 HOH HOH . I 3 HOH A 41 641 174 HOH HOH . I 3 HOH A 42 642 179 HOH HOH . I 3 HOH A 43 643 184 HOH HOH . I 3 HOH A 44 644 188 HOH HOH . I 3 HOH A 45 645 208 HOH HOH . I 3 HOH A 46 646 212 HOH HOH . I 3 HOH A 47 647 216 HOH HOH . I 3 HOH A 48 648 222 HOH HOH . I 3 HOH A 49 649 233 HOH HOH . I 3 HOH A 50 650 236 HOH HOH . I 3 HOH A 51 651 238 HOH HOH . J 3 HOH B 1 601 2 HOH HOH . J 3 HOH B 2 602 5 HOH HOH . J 3 HOH B 3 603 8 HOH HOH . J 3 HOH B 4 604 11 HOH HOH . J 3 HOH B 5 605 17 HOH HOH . J 3 HOH B 6 606 21 HOH HOH . J 3 HOH B 7 607 24 HOH HOH . J 3 HOH B 8 608 34 HOH HOH . J 3 HOH B 9 609 38 HOH HOH . J 3 HOH B 10 610 46 HOH HOH . J 3 HOH B 11 611 47 HOH HOH . J 3 HOH B 12 612 49 HOH HOH . J 3 HOH B 13 613 52 HOH HOH . J 3 HOH B 14 614 56 HOH HOH . J 3 HOH B 15 615 70 HOH HOH . J 3 HOH B 16 616 74 HOH HOH . J 3 HOH B 17 617 77 HOH HOH . J 3 HOH B 18 618 88 HOH HOH . J 3 HOH B 19 619 92 HOH HOH . J 3 HOH B 20 620 100 HOH HOH . J 3 HOH B 21 621 103 HOH HOH . J 3 HOH B 22 622 136 HOH HOH . J 3 HOH B 23 623 149 HOH HOH . J 3 HOH B 24 624 150 HOH HOH . J 3 HOH B 25 625 151 HOH HOH . J 3 HOH B 26 626 152 HOH HOH . J 3 HOH B 27 627 155 HOH HOH . J 3 HOH B 28 628 156 HOH HOH . J 3 HOH B 29 629 158 HOH HOH . J 3 HOH B 30 630 161 HOH HOH . J 3 HOH B 31 631 162 HOH HOH . J 3 HOH B 32 632 164 HOH HOH . J 3 HOH B 33 633 165 HOH HOH . J 3 HOH B 34 634 169 HOH HOH . J 3 HOH B 35 635 170 HOH HOH . J 3 HOH B 36 636 172 HOH HOH . J 3 HOH B 37 637 176 HOH HOH . J 3 HOH B 38 638 177 HOH HOH . J 3 HOH B 39 639 185 HOH HOH . J 3 HOH B 40 640 191 HOH HOH . J 3 HOH B 41 641 192 HOH HOH . J 3 HOH B 42 642 195 HOH HOH . J 3 HOH B 43 643 199 HOH HOH . J 3 HOH B 44 644 200 HOH HOH . J 3 HOH B 45 645 201 HOH HOH . J 3 HOH B 46 646 205 HOH HOH . J 3 HOH B 47 647 211 HOH HOH . J 3 HOH B 48 648 214 HOH HOH . J 3 HOH B 49 649 220 HOH HOH . J 3 HOH B 50 650 223 HOH HOH . J 3 HOH B 51 651 225 HOH HOH . J 3 HOH B 52 652 228 HOH HOH . J 3 HOH B 53 653 230 HOH HOH . J 3 HOH B 54 654 232 HOH HOH . K 3 HOH C 1 501 14 HOH HOH . K 3 HOH C 2 502 19 HOH HOH . K 3 HOH C 3 503 22 HOH HOH . K 3 HOH C 4 504 27 HOH HOH . K 3 HOH C 5 505 33 HOH HOH . K 3 HOH C 6 506 36 HOH HOH . K 3 HOH C 7 507 40 HOH HOH . K 3 HOH C 8 508 43 HOH HOH . K 3 HOH C 9 509 44 HOH HOH . K 3 HOH C 10 510 50 HOH HOH . K 3 HOH C 11 511 55 HOH HOH . K 3 HOH C 12 512 62 HOH HOH . K 3 HOH C 13 513 64 HOH HOH . K 3 HOH C 14 514 65 HOH HOH . K 3 HOH C 15 515 73 HOH HOH . K 3 HOH C 16 516 75 HOH HOH . K 3 HOH C 17 517 76 HOH HOH . K 3 HOH C 18 518 78 HOH HOH . K 3 HOH C 19 519 80 HOH HOH . K 3 HOH C 20 520 82 HOH HOH . K 3 HOH C 21 521 86 HOH HOH . K 3 HOH C 22 522 89 HOH HOH . K 3 HOH C 23 523 95 HOH HOH . K 3 HOH C 24 524 97 HOH HOH . K 3 HOH C 25 525 99 HOH HOH . K 3 HOH C 26 526 102 HOH HOH . K 3 HOH C 27 527 106 HOH HOH . K 3 HOH C 28 528 107 HOH HOH . K 3 HOH C 29 529 108 HOH HOH . K 3 HOH C 30 530 109 HOH HOH . K 3 HOH C 31 531 113 HOH HOH . K 3 HOH C 32 532 118 HOH HOH . K 3 HOH C 33 533 125 HOH HOH . K 3 HOH C 34 534 129 HOH HOH . K 3 HOH C 35 535 132 HOH HOH . K 3 HOH C 36 536 138 HOH HOH . K 3 HOH C 37 537 141 HOH HOH . K 3 HOH C 38 538 146 HOH HOH . K 3 HOH C 39 539 153 HOH HOH . K 3 HOH C 40 540 171 HOH HOH . K 3 HOH C 41 541 178 HOH HOH . K 3 HOH C 42 542 187 HOH HOH . K 3 HOH C 43 543 203 HOH HOH . K 3 HOH C 44 544 215 HOH HOH . K 3 HOH C 45 545 217 HOH HOH . K 3 HOH C 46 546 221 HOH HOH . K 3 HOH C 47 547 224 HOH HOH . K 3 HOH C 48 548 226 HOH HOH . K 3 HOH C 49 549 227 HOH HOH . K 3 HOH C 50 550 234 HOH HOH . L 3 HOH D 1 501 3 HOH HOH . L 3 HOH D 2 502 7 HOH HOH . L 3 HOH D 3 503 10 HOH HOH . L 3 HOH D 4 504 13 HOH HOH . L 3 HOH D 5 505 15 HOH HOH . L 3 HOH D 6 506 18 HOH HOH . L 3 HOH D 7 507 20 HOH HOH . L 3 HOH D 8 508 23 HOH HOH . L 3 HOH D 9 509 26 HOH HOH . L 3 HOH D 10 510 28 HOH HOH . L 3 HOH D 11 511 31 HOH HOH . L 3 HOH D 12 512 32 HOH HOH . L 3 HOH D 13 513 39 HOH HOH . L 3 HOH D 14 514 41 HOH HOH . L 3 HOH D 15 515 42 HOH HOH . L 3 HOH D 16 516 51 HOH HOH . L 3 HOH D 17 517 54 HOH HOH . L 3 HOH D 18 518 57 HOH HOH . L 3 HOH D 19 519 59 HOH HOH . L 3 HOH D 20 520 71 HOH HOH . L 3 HOH D 21 521 85 HOH HOH . L 3 HOH D 22 522 87 HOH HOH . L 3 HOH D 23 523 90 HOH HOH . L 3 HOH D 24 524 93 HOH HOH . L 3 HOH D 25 525 94 HOH HOH . L 3 HOH D 26 526 112 HOH HOH . L 3 HOH D 27 527 115 HOH HOH . L 3 HOH D 28 528 120 HOH HOH . L 3 HOH D 29 529 123 HOH HOH . L 3 HOH D 30 530 124 HOH HOH . L 3 HOH D 31 531 126 HOH HOH . L 3 HOH D 32 532 131 HOH HOH . L 3 HOH D 33 533 139 HOH HOH . L 3 HOH D 34 534 142 HOH HOH . L 3 HOH D 35 535 147 HOH HOH . L 3 HOH D 36 536 148 HOH HOH . L 3 HOH D 37 537 154 HOH HOH . L 3 HOH D 38 538 157 HOH HOH . L 3 HOH D 39 539 159 HOH HOH . L 3 HOH D 40 540 160 HOH HOH . L 3 HOH D 41 541 163 HOH HOH . L 3 HOH D 42 542 167 HOH HOH . L 3 HOH D 43 543 168 HOH HOH . L 3 HOH D 44 544 173 HOH HOH . L 3 HOH D 45 545 180 HOH HOH . L 3 HOH D 46 546 181 HOH HOH . L 3 HOH D 47 547 183 HOH HOH . L 3 HOH D 48 548 189 HOH HOH . L 3 HOH D 49 549 193 HOH HOH . L 3 HOH D 50 550 202 HOH HOH . L 3 HOH D 51 551 204 HOH HOH . L 3 HOH D 52 552 206 HOH HOH . L 3 HOH D 53 553 207 HOH HOH . L 3 HOH D 54 554 210 HOH HOH . L 3 HOH D 55 555 219 HOH HOH . L 3 HOH D 56 556 229 HOH HOH . L 3 HOH D 57 557 231 HOH HOH . L 3 HOH D 58 558 235 HOH HOH . L 3 HOH D 59 559 237 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 -37.892 6.677 27.073 1 45.38 ? N1 PLP 501 B 1 HETATM 2 C C2 PLP . . . F 2 -37.434 5.447 26.67 1 45.07 ? C2 PLP 501 B 1 HETATM 3 C C2A PLP . . . F 2 -37.851 4.909 25.329 1 37.24 ? C2A PLP 501 B 1 HETATM 4 C C3 PLP . . . F 2 -36.582 4.719 27.488 1 46.13 ? C3 PLP 501 B 1 HETATM 5 O O3 PLP . . . F 2 -36.053 3.523 27.042 1 45.27 ? O3 PLP 501 B 1 HETATM 6 C C4 PLP . . . F 2 -36.188 5.206 28.728 1 48.03 ? C4 PLP 501 B 1 HETATM 7 C C4A PLP . . . F 2 -35.429 3.966 29.191 1 51.18 ? C4A PLP 501 B 1 HETATM 8 C C5 PLP . . . F 2 -36.67 6.462 29.116 1 46.85 ? C5 PLP 501 B 1 HETATM 9 C C6 PLP . . . F 2 -37.518 7.179 28.29 1 42.46 ? C6 PLP 501 B 1 HETATM 10 C C5A PLP . . . F 2 -36.323 7.08 30.451 1 45.5 ? C5A PLP 501 B 1 HETATM 11 O O4P PLP . . . F 2 -34.955 6.988 30.762 1 44.42 ? O4P PLP 501 B 1 HETATM 12 P P PLP . . . F 2 -34.52 6.908 32.311 1 43.36 ? P PLP 501 B 1 HETATM 13 O O1P PLP . . . F 2 -33.102 7.405 32.418 1 31.42 ? O1P PLP 501 B 1 HETATM 14 O O2P PLP . . . F 2 -34.656 5.468 32.755 1 41.06 ? O2P PLP 501 B 1 HETATM 15 O O3P PLP . . . F 2 -35.426 7.739 33.202 1 39.4 ? O3P PLP 501 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 15 #