data_5GRF # _model_server_result.job_id pbt6LAqicG9kZsd22nJycw _model_server_result.datetime_utc '2024-12-27 03:34:34' _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 5grf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 5GRF # _exptl.entry_id 5GRF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 192.124 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CITRIC ACID' _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 5GRF _cell.length_a 114.336 _cell.length_b 114.336 _cell.length_c 143.901 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GRF _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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,G _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 B O ARG 272 B ARG 272 1_555 E MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc2 C O6 CIT . B CIT 401 1_555 E MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc3 D O2B ADP . B ADP 402 1_555 E MG MG . B MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc4 E MG MG . B MG 403 1_555 G O HOH . B HOH 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? metalc ? metalc5 E MG MG . B MG 403 1_555 G O HOH . B HOH 586 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? # _chem_comp.formula 'C6 H8 O7' _chem_comp.formula_weight 192.124 _chem_comp.id CIT _chem_comp.mon_nstd_flag . _chem_comp.name 'CITRIC ACID' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 O1 CIT doub 114 n n C1 O2 CIT sing 115 n n C1 C2 CIT sing 116 n n O2 HO2 CIT sing 117 n n C2 C3 CIT sing 118 n n C2 H21 CIT sing 119 n n C2 H22 CIT sing 120 n n C3 O7 CIT sing 121 n n C3 C4 CIT sing 122 n n C3 C6 CIT sing 123 n n O7 HO7 CIT sing 124 n n C4 C5 CIT sing 125 n n C4 H41 CIT sing 126 n n C4 H42 CIT sing 127 n n C5 O3 CIT doub 128 n n C5 O4 CIT sing 129 n n O4 HO4 CIT sing 130 n n C6 O5 CIT doub 131 n n C6 O6 CIT sing 132 n n O6 HO6 CIT sing 133 n n # _atom_sites.entry_id 5GRF _atom_sites.fract_transf_matrix[1][1] 0.008746 _atom_sites.fract_transf_matrix[1][2] 0.00505 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010099 _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] 0.006949 _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 3 CIT B 1 401 1 CIT CIT . D 4 ADP B 1 402 1 ADP ADP . E 5 MG B 1 403 1 MG MG . F 6 HOH A 1 401 4 HOH HOH . F 6 HOH A 2 402 11 HOH HOH . F 6 HOH A 3 403 40 HOH HOH . F 6 HOH A 4 404 77 HOH HOH . F 6 HOH A 5 405 58 HOH HOH . F 6 HOH A 6 406 128 HOH HOH . F 6 HOH A 7 407 12 HOH HOH . F 6 HOH A 8 408 41 HOH HOH . F 6 HOH A 9 409 82 HOH HOH . F 6 HOH A 10 410 64 HOH HOH . F 6 HOH A 11 411 96 HOH HOH . F 6 HOH A 12 412 9 HOH HOH . F 6 HOH A 13 413 73 HOH HOH . F 6 HOH A 14 414 117 HOH HOH . F 6 HOH A 15 415 114 HOH HOH . F 6 HOH A 16 416 91 HOH HOH . F 6 HOH A 17 417 108 HOH HOH . F 6 HOH A 18 418 68 HOH HOH . F 6 HOH A 19 419 98 HOH HOH . F 6 HOH A 20 420 85 HOH HOH . F 6 HOH A 21 421 75 HOH HOH . F 6 HOH A 22 422 71 HOH HOH . F 6 HOH A 23 423 56 HOH HOH . F 6 HOH A 24 424 109 HOH HOH . G 6 HOH B 1 501 21 HOH HOH . G 6 HOH B 2 502 90 HOH HOH . G 6 HOH B 3 503 88 HOH HOH . G 6 HOH B 4 504 28 HOH HOH . G 6 HOH B 5 505 112 HOH HOH . G 6 HOH B 6 506 37 HOH HOH . G 6 HOH B 7 507 36 HOH HOH . G 6 HOH B 8 508 13 HOH HOH . G 6 HOH B 9 509 18 HOH HOH . G 6 HOH B 10 510 99 HOH HOH . G 6 HOH B 11 511 22 HOH HOH . G 6 HOH B 12 512 93 HOH HOH . G 6 HOH B 13 513 5 HOH HOH . G 6 HOH B 14 514 57 HOH HOH . G 6 HOH B 15 515 42 HOH HOH . G 6 HOH B 16 516 38 HOH HOH . G 6 HOH B 17 517 6 HOH HOH . G 6 HOH B 18 518 27 HOH HOH . G 6 HOH B 19 519 131 HOH HOH . G 6 HOH B 20 520 10 HOH HOH . G 6 HOH B 21 521 30 HOH HOH . G 6 HOH B 22 522 124 HOH HOH . G 6 HOH B 23 523 7 HOH HOH . G 6 HOH B 24 524 49 HOH HOH . G 6 HOH B 25 525 53 HOH HOH . G 6 HOH B 26 526 54 HOH HOH . G 6 HOH B 27 527 69 HOH HOH . G 6 HOH B 28 528 66 HOH HOH . G 6 HOH B 29 529 23 HOH HOH . G 6 HOH B 30 530 130 HOH HOH . G 6 HOH B 31 531 52 HOH HOH . G 6 HOH B 32 532 132 HOH HOH . G 6 HOH B 33 533 43 HOH HOH . G 6 HOH B 34 534 102 HOH HOH . G 6 HOH B 35 535 31 HOH HOH . G 6 HOH B 36 536 110 HOH HOH . G 6 HOH B 37 537 63 HOH HOH . G 6 HOH B 38 538 81 HOH HOH . G 6 HOH B 39 539 39 HOH HOH . G 6 HOH B 40 540 24 HOH HOH . G 6 HOH B 41 541 8 HOH HOH . G 6 HOH B 42 542 19 HOH HOH . G 6 HOH B 43 543 97 HOH HOH . G 6 HOH B 44 544 100 HOH HOH . G 6 HOH B 45 545 84 HOH HOH . G 6 HOH B 46 546 129 HOH HOH . G 6 HOH B 47 547 26 HOH HOH . G 6 HOH B 48 548 55 HOH HOH . G 6 HOH B 49 549 29 HOH HOH . G 6 HOH B 50 550 62 HOH HOH . G 6 HOH B 51 551 111 HOH HOH . G 6 HOH B 52 552 48 HOH HOH . G 6 HOH B 53 553 95 HOH HOH . G 6 HOH B 54 554 61 HOH HOH . G 6 HOH B 55 555 14 HOH HOH . G 6 HOH B 56 556 33 HOH HOH . G 6 HOH B 57 557 20 HOH HOH . G 6 HOH B 58 558 51 HOH HOH . G 6 HOH B 59 559 25 HOH HOH . G 6 HOH B 60 560 65 HOH HOH . G 6 HOH B 61 561 115 HOH HOH . G 6 HOH B 62 562 15 HOH HOH . G 6 HOH B 63 563 44 HOH HOH . G 6 HOH B 64 564 45 HOH HOH . G 6 HOH B 65 565 133 HOH HOH . G 6 HOH B 66 566 3 HOH HOH . G 6 HOH B 67 567 2 HOH HOH . G 6 HOH B 68 568 47 HOH HOH . G 6 HOH B 69 569 35 HOH HOH . G 6 HOH B 70 570 76 HOH HOH . G 6 HOH B 71 571 67 HOH HOH . G 6 HOH B 72 572 34 HOH HOH . G 6 HOH B 73 573 70 HOH HOH . G 6 HOH B 74 574 103 HOH HOH . G 6 HOH B 75 575 116 HOH HOH . G 6 HOH B 76 576 50 HOH HOH . G 6 HOH B 77 577 134 HOH HOH . G 6 HOH B 78 578 89 HOH HOH . G 6 HOH B 79 579 126 HOH HOH . G 6 HOH B 80 580 46 HOH HOH . G 6 HOH B 81 581 32 HOH HOH . G 6 HOH B 82 582 107 HOH HOH . G 6 HOH B 83 583 80 HOH HOH . G 6 HOH B 84 584 78 HOH HOH . G 6 HOH B 85 585 1 HOH HOH . G 6 HOH B 86 586 127 HOH HOH . G 6 HOH B 87 587 94 HOH HOH . G 6 HOH B 88 588 16 HOH HOH . G 6 HOH B 89 589 72 HOH HOH . G 6 HOH B 90 590 104 HOH HOH . G 6 HOH B 91 591 122 HOH HOH . G 6 HOH B 92 592 121 HOH HOH . G 6 HOH B 93 593 101 HOH HOH . G 6 HOH B 94 594 106 HOH HOH . G 6 HOH B 95 595 113 HOH HOH . G 6 HOH B 96 596 120 HOH HOH . G 6 HOH B 97 597 79 HOH HOH . G 6 HOH B 98 598 74 HOH HOH . G 6 HOH B 99 599 59 HOH HOH . G 6 HOH B 100 600 92 HOH HOH . G 6 HOH B 101 601 87 HOH HOH . G 6 HOH B 102 602 118 HOH HOH . G 6 HOH B 103 603 119 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 C C1 CIT . . . C 3 46.613 -16.454 -7.83 1 46.14 ? C1 CIT 401 B 1 HETATM 2 O O1 CIT . . . C 3 45.674 -16.006 -8.539 1 44.78 ? O1 CIT 401 B 1 HETATM 3 O O2 CIT . . . C 3 47.664 -16.85 -8.386 1 49.35 ? O2 CIT 401 B 1 HETATM 4 C C2 CIT . . . C 3 46.476 -16.542 -6.322 1 50.4 ? C2 CIT 401 B 1 HETATM 5 C C3 CIT . . . C 3 46.421 -15.184 -5.608 1 54.43 ? C3 CIT 401 B 1 HETATM 6 O O7 CIT . . . C 3 47.145 -14.182 -6.305 1 49.57 ? O7 CIT 401 B 1 HETATM 7 C C4 CIT . . . C 3 44.991 -14.687 -5.445 1 50.84 ? C4 CIT 401 B 1 HETATM 8 C C5 CIT . . . C 3 44.899 -13.444 -4.573 1 54.39 ? C5 CIT 401 B 1 HETATM 9 O O3 CIT . . . C 3 45.901 -12.7 -4.374 1 55.71 ? O3 CIT 401 B 1 HETATM 10 O O4 CIT . . . C 3 43.803 -13.156 -4.031 1 48.12 ? O4 CIT 401 B 1 HETATM 11 C C6 CIT . . . C 3 47.043 -15.36 -4.232 1 59.29 ? C6 CIT 401 B 1 HETATM 12 O O5 CIT . . . C 3 48.222 -14.957 -4.006 1 52.36 ? O5 CIT 401 B 1 HETATM 13 O O6 CIT . . . C 3 46.382 -15.907 -3.305 1 61.05 ? O6 CIT 401 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 219 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #