data_4LMA # _model_server_result.job_id 6I01bNbFeqhKVolIb55lsg _model_server_result.datetime_utc '2024-12-04 03:39:38' _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 4lma # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":402}' # _entry.id 4LMA # _exptl.entry_id 4LMA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _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 4LMA _cell.length_a 56.564 _cell.length_b 93.83 _cell.length_c 125.307 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LMA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,G,H,I _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 ? 3 E N N ? 3 G 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 53 A LYS 46 1_555 E C4A PLP . A PLP 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.245 ? covale ? covale2 B NZ LYS 53 B LYS 46 1_555 G C4A PLP . B PLP 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.537 ? # _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 281 n y N1 C6 PLP sing 282 n y C2 C2A PLP sing 283 n n C2 C3 PLP sing 284 n y C2A H2A1 PLP sing 285 n n C2A H2A2 PLP sing 286 n n C2A H2A3 PLP sing 287 n n C3 O3 PLP sing 288 n n C3 C4 PLP doub 289 n y O3 HO3 PLP sing 290 n n C4 C4A PLP sing 291 n n C4 C5 PLP sing 292 n y C4A O4A PLP doub 293 n n C4A H4A PLP sing 294 n n C5 C6 PLP doub 295 n y C5 C5A PLP sing 296 n n C6 H6 PLP sing 297 n n C5A O4P PLP sing 298 n n C5A H5A1 PLP sing 299 n n C5A H5A2 PLP sing 300 n n O4P P PLP sing 301 n n P O1P PLP doub 302 n n P O2P PLP sing 303 n n P O3P PLP sing 304 n n O2P HOP2 PLP sing 305 n n O3P HOP3 PLP sing 306 n n # _atom_sites.entry_id 4LMA _atom_sites.fract_transf_matrix[1][1] 0.017679 _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] 0.010658 _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] 0.00798 _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 MPD A 1 401 401 MPD MPD . D 2 MPD A 1 402 400 MPD MPD . E 3 PLP A 1 403 350 PLP PLP . F 2 MPD B 1 401 400 MPD MPD . G 3 PLP B 1 402 350 PLP PLP . H 4 HOH A 1 501 3 HOH HOH . H 4 HOH A 2 502 6 HOH HOH . H 4 HOH A 3 503 8 HOH HOH . H 4 HOH A 4 504 9 HOH HOH . H 4 HOH A 5 505 10 HOH HOH . H 4 HOH A 6 506 11 HOH HOH . H 4 HOH A 7 507 13 HOH HOH . H 4 HOH A 8 508 15 HOH HOH . H 4 HOH A 9 509 16 HOH HOH . H 4 HOH A 10 510 18 HOH HOH . H 4 HOH A 11 511 20 HOH HOH . H 4 HOH A 12 512 21 HOH HOH . H 4 HOH A 13 513 28 HOH HOH . H 4 HOH A 14 514 29 HOH HOH . H 4 HOH A 15 515 30 HOH HOH . H 4 HOH A 16 516 32 HOH HOH . H 4 HOH A 17 517 34 HOH HOH . H 4 HOH A 18 518 35 HOH HOH . H 4 HOH A 19 519 38 HOH HOH . H 4 HOH A 20 520 40 HOH HOH . H 4 HOH A 21 521 41 HOH HOH . H 4 HOH A 22 522 42 HOH HOH . H 4 HOH A 23 523 43 HOH HOH . H 4 HOH A 24 524 45 HOH HOH . H 4 HOH A 25 525 47 HOH HOH . H 4 HOH A 26 526 48 HOH HOH . H 4 HOH A 27 527 50 HOH HOH . H 4 HOH A 28 528 53 HOH HOH . H 4 HOH A 29 529 54 HOH HOH . H 4 HOH A 30 530 1 HOH HOH . H 4 HOH A 31 531 57 HOH HOH . H 4 HOH A 32 532 58 HOH HOH . H 4 HOH A 33 533 61 HOH HOH . H 4 HOH A 34 534 62 HOH HOH . H 4 HOH A 35 535 65 HOH HOH . H 4 HOH A 36 536 66 HOH HOH . H 4 HOH A 37 537 67 HOH HOH . H 4 HOH A 38 538 68 HOH HOH . H 4 HOH A 39 539 70 HOH HOH . H 4 HOH A 40 540 71 HOH HOH . H 4 HOH A 41 541 72 HOH HOH . H 4 HOH A 42 542 76 HOH HOH . H 4 HOH A 43 543 78 HOH HOH . H 4 HOH A 44 544 79 HOH HOH . H 4 HOH A 45 545 80 HOH HOH . H 4 HOH A 46 546 81 HOH HOH . H 4 HOH A 47 547 82 HOH HOH . H 4 HOH A 48 548 86 HOH HOH . H 4 HOH A 49 549 88 HOH HOH . H 4 HOH A 50 550 90 HOH HOH . H 4 HOH A 51 551 91 HOH HOH . H 4 HOH A 52 552 92 HOH HOH . H 4 HOH A 53 553 93 HOH HOH . H 4 HOH A 54 554 96 HOH HOH . H 4 HOH A 55 555 98 HOH HOH . H 4 HOH A 56 556 100 HOH HOH . H 4 HOH A 57 557 104 HOH HOH . H 4 HOH A 58 558 107 HOH HOH . H 4 HOH A 59 559 108 HOH HOH . H 4 HOH A 60 560 118 HOH HOH . H 4 HOH A 61 561 121 HOH HOH . H 4 HOH A 62 562 124 HOH HOH . H 4 HOH A 63 563 128 HOH HOH . H 4 HOH A 64 564 129 HOH HOH . H 4 HOH A 65 565 131 HOH HOH . H 4 HOH A 66 566 132 HOH HOH . H 4 HOH A 67 567 135 HOH HOH . H 4 HOH A 68 568 137 HOH HOH . H 4 HOH A 69 569 140 HOH HOH . H 4 HOH A 70 570 144 HOH HOH . H 4 HOH A 71 571 146 HOH HOH . H 4 HOH A 72 572 151 HOH HOH . H 4 HOH A 73 573 152 HOH HOH . H 4 HOH A 74 574 159 HOH HOH . H 4 HOH A 75 575 161 HOH HOH . H 4 HOH A 76 576 163 HOH HOH . H 4 HOH A 77 577 164 HOH HOH . H 4 HOH A 78 578 166 HOH HOH . H 4 HOH A 79 579 167 HOH HOH . H 4 HOH A 80 580 169 HOH HOH . H 4 HOH A 81 581 170 HOH HOH . H 4 HOH A 82 582 176 HOH HOH . H 4 HOH A 83 583 178 HOH HOH . H 4 HOH A 84 584 182 HOH HOH . H 4 HOH A 85 585 184 HOH HOH . H 4 HOH A 86 586 185 HOH HOH . H 4 HOH A 87 587 186 HOH HOH . H 4 HOH A 88 588 189 HOH HOH . H 4 HOH A 89 589 191 HOH HOH . H 4 HOH A 90 590 193 HOH HOH . H 4 HOH A 91 591 194 HOH HOH . H 4 HOH A 92 592 196 HOH HOH . H 4 HOH A 93 593 197 HOH HOH . I 4 HOH B 1 501 177 HOH HOH . I 4 HOH B 2 502 4 HOH HOH . I 4 HOH B 3 503 5 HOH HOH . I 4 HOH B 4 504 7 HOH HOH . I 4 HOH B 5 505 12 HOH HOH . I 4 HOH B 6 506 14 HOH HOH . I 4 HOH B 7 507 17 HOH HOH . I 4 HOH B 8 508 19 HOH HOH . I 4 HOH B 9 509 22 HOH HOH . I 4 HOH B 10 510 23 HOH HOH . I 4 HOH B 11 511 24 HOH HOH . I 4 HOH B 12 512 25 HOH HOH . I 4 HOH B 13 513 26 HOH HOH . I 4 HOH B 14 514 27 HOH HOH . I 4 HOH B 15 515 31 HOH HOH . I 4 HOH B 16 516 33 HOH HOH . I 4 HOH B 17 517 36 HOH HOH . I 4 HOH B 18 518 37 HOH HOH . I 4 HOH B 19 519 39 HOH HOH . I 4 HOH B 20 520 44 HOH HOH . I 4 HOH B 21 521 46 HOH HOH . I 4 HOH B 22 522 49 HOH HOH . I 4 HOH B 23 523 51 HOH HOH . I 4 HOH B 24 524 52 HOH HOH . I 4 HOH B 25 525 55 HOH HOH . I 4 HOH B 26 526 56 HOH HOH . I 4 HOH B 27 527 59 HOH HOH . I 4 HOH B 28 528 60 HOH HOH . I 4 HOH B 29 529 63 HOH HOH . I 4 HOH B 30 530 64 HOH HOH . I 4 HOH B 31 531 69 HOH HOH . I 4 HOH B 32 532 73 HOH HOH . I 4 HOH B 33 533 74 HOH HOH . I 4 HOH B 34 534 75 HOH HOH . I 4 HOH B 35 535 77 HOH HOH . I 4 HOH B 36 536 83 HOH HOH . I 4 HOH B 37 537 84 HOH HOH . I 4 HOH B 38 538 85 HOH HOH . I 4 HOH B 39 539 87 HOH HOH . I 4 HOH B 40 540 89 HOH HOH . I 4 HOH B 41 541 94 HOH HOH . I 4 HOH B 42 542 95 HOH HOH . I 4 HOH B 43 543 97 HOH HOH . I 4 HOH B 44 544 99 HOH HOH . I 4 HOH B 45 545 101 HOH HOH . I 4 HOH B 46 546 102 HOH HOH . I 4 HOH B 47 547 103 HOH HOH . I 4 HOH B 48 548 105 HOH HOH . I 4 HOH B 49 549 106 HOH HOH . I 4 HOH B 50 550 109 HOH HOH . I 4 HOH B 51 551 110 HOH HOH . I 4 HOH B 52 552 111 HOH HOH . I 4 HOH B 53 553 112 HOH HOH . I 4 HOH B 54 554 113 HOH HOH . I 4 HOH B 55 555 114 HOH HOH . I 4 HOH B 56 556 115 HOH HOH . I 4 HOH B 57 557 116 HOH HOH . I 4 HOH B 58 558 117 HOH HOH . I 4 HOH B 59 559 119 HOH HOH . I 4 HOH B 60 560 120 HOH HOH . I 4 HOH B 61 561 122 HOH HOH . I 4 HOH B 62 562 123 HOH HOH . I 4 HOH B 63 563 125 HOH HOH . I 4 HOH B 64 564 126 HOH HOH . I 4 HOH B 65 565 127 HOH HOH . I 4 HOH B 66 566 2 HOH HOH . I 4 HOH B 67 567 130 HOH HOH . I 4 HOH B 68 568 133 HOH HOH . I 4 HOH B 69 569 134 HOH HOH . I 4 HOH B 70 570 136 HOH HOH . I 4 HOH B 71 571 138 HOH HOH . I 4 HOH B 72 572 139 HOH HOH . I 4 HOH B 73 573 141 HOH HOH . I 4 HOH B 74 574 142 HOH HOH . I 4 HOH B 75 575 143 HOH HOH . I 4 HOH B 76 576 145 HOH HOH . I 4 HOH B 77 577 147 HOH HOH . I 4 HOH B 78 578 148 HOH HOH . I 4 HOH B 79 579 150 HOH HOH . I 4 HOH B 80 580 153 HOH HOH . I 4 HOH B 81 581 155 HOH HOH . I 4 HOH B 82 582 156 HOH HOH . I 4 HOH B 83 583 157 HOH HOH . I 4 HOH B 84 584 158 HOH HOH . I 4 HOH B 85 585 160 HOH HOH . I 4 HOH B 86 586 162 HOH HOH . I 4 HOH B 87 587 165 HOH HOH . I 4 HOH B 88 588 168 HOH HOH . I 4 HOH B 89 589 171 HOH HOH . I 4 HOH B 90 590 172 HOH HOH . I 4 HOH B 91 591 173 HOH HOH . I 4 HOH B 92 592 174 HOH HOH . I 4 HOH B 93 593 175 HOH HOH . I 4 HOH B 94 594 179 HOH HOH . I 4 HOH B 95 595 180 HOH HOH . I 4 HOH B 96 596 181 HOH HOH . I 4 HOH B 97 597 183 HOH HOH . I 4 HOH B 98 598 187 HOH HOH . I 4 HOH B 99 599 188 HOH HOH . I 4 HOH B 100 600 190 HOH HOH . I 4 HOH B 101 601 192 HOH HOH . I 4 HOH B 102 602 195 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 . . . G 3 33.612 2.87 13.118 1 29.98 ? N1 PLP 402 B 1 HETATM 2 C C2 PLP . . . G 3 32.333 2.656 12.712 1 30.27 ? C2 PLP 402 B 1 HETATM 3 C C2A PLP . . . G 3 31.672 3.608 11.739 1 29.36 ? C2A PLP 402 B 1 HETATM 4 C C3 PLP . . . G 3 31.605 1.476 13.236 1 29.49 ? C3 PLP 402 B 1 HETATM 5 O O3 PLP . . . G 3 30.328 1.207 12.864 1 28.92 ? O3 PLP 402 B 1 HETATM 6 C C4 PLP . . . G 3 32.337 0.601 14.19 1 29.91 ? C4 PLP 402 B 1 HETATM 7 C C4A PLP . . . G 3 31.703 -0.594 14.761 1 29.16 ? C4A PLP 402 B 1 HETATM 8 C C5 PLP . . . G 3 33.733 0.936 14.547 1 29.32 ? C5 PLP 402 B 1 HETATM 9 C C6 PLP . . . G 3 34.286 2.076 13.976 1 29.92 ? C6 PLP 402 B 1 HETATM 10 C C5A PLP . . . G 3 34.55 0.09 15.515 1 29.68 ? C5A PLP 402 B 1 HETATM 11 O O4P PLP . . . G 3 34.289 -1.32 15.418 1 28.01 ? O4P PLP 402 B 1 HETATM 12 P P PLP . . . G 3 34.244 -2.251 16.741 1 27.28 ? P PLP 402 B 1 HETATM 13 O O1P PLP . . . G 3 34.433 -3.664 16.245 1 27.53 ? O1P PLP 402 B 1 HETATM 14 O O2P PLP . . . G 3 35.386 -1.729 17.576 1 27.2 ? O2P PLP 402 B 1 HETATM 15 O O3P PLP . . . G 3 32.875 -2.042 17.338 1 26.37 ? O3P PLP 402 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #