data_1RFV # _model_server_result.job_id 9uEahzZMF4UWSkCOVVsmuw _model_server_result.datetime_utc '2024-11-25 06:37:06' _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 1rfv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 1RFV # _exptl.entry_id 1RFV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 1RFV _cell.length_a 59.066 _cell.length_b 93.942 _cell.length_c 128.743 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RFV _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 _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 D N N ? 3 F 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 metalc ? metalc1 D O2B ADP . A ADP 401 1_555 C ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc2 F O2B ADP . B ADP 1401 1_555 E ZN ZN . B ZN 1402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 1RFV _atom_sites.fract_transf_matrix[1][1] 0.01693 _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] 0.010645 _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] 0.007767 _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 ZN A 1 402 402 ZN ZN2 . D 3 ADP A 1 401 401 ADP ADP . E 2 ZN B 1 1402 402 ZN ZN2 . F 3 ADP B 1 1401 401 ADP ADP . G 4 HOH A 1 403 2 HOH WAT . G 4 HOH A 2 404 3 HOH WAT . G 4 HOH A 3 405 4 HOH WAT . G 4 HOH A 4 406 11 HOH WAT . G 4 HOH A 5 407 12 HOH WAT . G 4 HOH A 6 408 13 HOH WAT . G 4 HOH A 7 409 14 HOH WAT . G 4 HOH A 8 410 16 HOH WAT . G 4 HOH A 9 411 17 HOH WAT . G 4 HOH A 10 412 18 HOH WAT . G 4 HOH A 11 413 19 HOH WAT . G 4 HOH A 12 414 22 HOH WAT . G 4 HOH A 13 415 25 HOH WAT . G 4 HOH A 14 416 26 HOH WAT . G 4 HOH A 15 417 28 HOH WAT . G 4 HOH A 16 418 29 HOH WAT . G 4 HOH A 17 419 32 HOH WAT . G 4 HOH A 18 420 33 HOH WAT . G 4 HOH A 19 421 34 HOH WAT . G 4 HOH A 20 422 35 HOH WAT . G 4 HOH A 21 423 40 HOH WAT . G 4 HOH A 22 424 41 HOH WAT . G 4 HOH A 23 425 43 HOH WAT . G 4 HOH A 24 426 47 HOH WAT . G 4 HOH A 25 427 49 HOH WAT . G 4 HOH A 26 428 50 HOH WAT . G 4 HOH A 27 429 51 HOH WAT . G 4 HOH A 28 430 54 HOH WAT . G 4 HOH A 29 431 55 HOH WAT . G 4 HOH A 30 432 58 HOH WAT . G 4 HOH A 31 433 60 HOH WAT . G 4 HOH A 32 434 61 HOH WAT . G 4 HOH A 33 435 63 HOH WAT . G 4 HOH A 34 436 70 HOH WAT . G 4 HOH A 35 437 71 HOH WAT . G 4 HOH A 36 438 73 HOH WAT . G 4 HOH A 37 439 74 HOH WAT . G 4 HOH A 38 440 75 HOH WAT . G 4 HOH A 39 441 76 HOH WAT . G 4 HOH A 40 442 77 HOH WAT . G 4 HOH A 41 443 87 HOH WAT . G 4 HOH A 42 444 88 HOH WAT . G 4 HOH A 43 445 89 HOH WAT . G 4 HOH A 44 446 91 HOH WAT . G 4 HOH A 45 447 92 HOH WAT . G 4 HOH A 46 448 93 HOH WAT . G 4 HOH A 47 449 94 HOH WAT . G 4 HOH A 48 450 98 HOH WAT . G 4 HOH A 49 451 99 HOH WAT . G 4 HOH A 50 452 101 HOH WAT . G 4 HOH A 51 453 102 HOH WAT . G 4 HOH A 52 454 104 HOH WAT . G 4 HOH A 53 455 105 HOH WAT . G 4 HOH A 54 456 106 HOH WAT . G 4 HOH A 55 457 108 HOH WAT . G 4 HOH A 56 458 110 HOH WAT . G 4 HOH A 57 459 115 HOH WAT . G 4 HOH A 58 460 116 HOH WAT . G 4 HOH A 59 461 118 HOH WAT . G 4 HOH A 60 462 120 HOH WAT . G 4 HOH A 61 463 121 HOH WAT . G 4 HOH A 62 464 122 HOH WAT . G 4 HOH A 63 465 124 HOH WAT . G 4 HOH A 64 466 125 HOH WAT . G 4 HOH A 65 467 127 HOH WAT . G 4 HOH A 66 468 128 HOH WAT . G 4 HOH A 67 469 130 HOH WAT . G 4 HOH A 68 470 138 HOH WAT . H 4 HOH B 1 1403 1 HOH WAT . H 4 HOH B 2 1404 5 HOH WAT . H 4 HOH B 3 1405 6 HOH WAT . H 4 HOH B 4 1406 7 HOH WAT . H 4 HOH B 5 1407 8 HOH WAT . H 4 HOH B 6 1408 9 HOH WAT . H 4 HOH B 7 1409 10 HOH WAT . H 4 HOH B 8 1410 15 HOH WAT . H 4 HOH B 9 1411 20 HOH WAT . H 4 HOH B 10 1412 21 HOH WAT . H 4 HOH B 11 1413 23 HOH WAT . H 4 HOH B 12 1414 24 HOH WAT . H 4 HOH B 13 1415 27 HOH WAT . H 4 HOH B 14 1416 30 HOH WAT . H 4 HOH B 15 1417 31 HOH WAT . H 4 HOH B 16 1418 36 HOH WAT . H 4 HOH B 17 1419 37 HOH WAT . H 4 HOH B 18 1420 38 HOH WAT . H 4 HOH B 19 1421 39 HOH WAT . H 4 HOH B 20 1422 42 HOH WAT . H 4 HOH B 21 1423 44 HOH WAT . H 4 HOH B 22 1424 45 HOH WAT . H 4 HOH B 23 1425 46 HOH WAT . H 4 HOH B 24 1426 48 HOH WAT . H 4 HOH B 25 1427 52 HOH WAT . H 4 HOH B 26 1428 53 HOH WAT . H 4 HOH B 27 1429 56 HOH WAT . H 4 HOH B 28 1430 57 HOH WAT . H 4 HOH B 29 1431 59 HOH WAT . H 4 HOH B 30 1432 62 HOH WAT . H 4 HOH B 31 1433 64 HOH WAT . H 4 HOH B 32 1434 65 HOH WAT . H 4 HOH B 33 1435 66 HOH WAT . H 4 HOH B 34 1436 67 HOH WAT . H 4 HOH B 35 1437 68 HOH WAT . H 4 HOH B 36 1438 69 HOH WAT . H 4 HOH B 37 1439 72 HOH WAT . H 4 HOH B 38 1440 78 HOH WAT . H 4 HOH B 39 1441 79 HOH WAT . H 4 HOH B 40 1442 80 HOH WAT . H 4 HOH B 41 1443 81 HOH WAT . H 4 HOH B 42 1444 82 HOH WAT . H 4 HOH B 43 1445 83 HOH WAT . H 4 HOH B 44 1446 84 HOH WAT . H 4 HOH B 45 1447 85 HOH WAT . H 4 HOH B 46 1448 86 HOH WAT . H 4 HOH B 47 1449 90 HOH WAT . H 4 HOH B 48 1450 95 HOH WAT . H 4 HOH B 49 1451 96 HOH WAT . H 4 HOH B 50 1452 97 HOH WAT . H 4 HOH B 51 1453 100 HOH WAT . H 4 HOH B 52 1454 103 HOH WAT . H 4 HOH B 53 1455 107 HOH WAT . H 4 HOH B 54 1456 109 HOH WAT . H 4 HOH B 55 1457 111 HOH WAT . H 4 HOH B 56 1458 112 HOH WAT . H 4 HOH B 57 1459 113 HOH WAT . H 4 HOH B 58 1460 114 HOH WAT . H 4 HOH B 59 1461 117 HOH WAT . H 4 HOH B 60 1462 119 HOH WAT . H 4 HOH B 61 1463 123 HOH WAT . H 4 HOH B 62 1464 126 HOH WAT . H 4 HOH B 63 1465 129 HOH WAT . H 4 HOH B 64 1466 131 HOH WAT . H 4 HOH B 65 1467 132 HOH WAT . H 4 HOH B 66 1468 133 HOH WAT . H 4 HOH B 67 1469 134 HOH WAT . H 4 HOH B 68 1470 135 HOH WAT . H 4 HOH B 69 1471 136 HOH WAT . H 4 HOH B 70 1472 137 HOH WAT . # 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 P PB ADP . . . D 3 27.086 -3.885 61.088 1 58.08 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . D 3 26.883 -4.473 62.473 1 54.17 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . D 3 28.567 -4.116 60.508 1 54.05 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . D 3 26.029 -4.386 60.144 1 51.18 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . D 3 25.881 -1.364 61.21 1 55.18 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . D 3 24.883 -1.975 61.947 1 50.63 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . D 3 25.146 -0.836 59.95 1 52.81 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . D 3 27.003 -2.355 60.989 1 52.67 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . D 3 26.805 -0.41 62.103 1 48.75 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . D 3 26.557 -0.341 63.378 1 39.21 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . D 3 27.204 0.789 64.043 1 38.31 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . D 3 26.261 1.74 63.672 1 37.29 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . D 3 27.085 0.587 65.581 1 38.06 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . D 3 28.169 1.266 66.307 1 40.28 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . D 3 25.737 1.182 65.917 1 37.17 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . D 3 25.703 1.788 67.2 1 40.11 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . D 3 25.426 2.121 64.753 1 34.48 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . D 3 23.975 2.007 64.328 1 31.84 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . D 3 23.524 1.505 63.134 1 28.95 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . D 3 22.187 1.569 63.103 1 30.76 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . D 3 21.764 2.104 64.233 1 29.89 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . D 3 20.514 2.419 64.783 1 28.41 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . D 3 19.391 2.206 64.067 1 23.59 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . D 3 20.437 2.983 66.046 1 30.09 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . D 3 21.552 3.22 66.795 1 30.28 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . D 3 22.761 2.921 66.266 1 28.92 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . D 3 22.915 2.36 65.035 1 30.04 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #