data_4NU1 # _model_server_result.job_id pbbhsklSJ5_vtqhrGXt2XA _model_server_result.datetime_utc '2024-10-11 00:31:52' _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 4nu1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":405}' # _entry.id 4NU1 # _exptl.entry_id 4NU1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 4NU1 _cell.length_a 80.997 _cell.length_b 80.997 _cell.length_c 280.53 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NU1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _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,J,K _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 5 _struct_asym.id G _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 covale ? covale1 A C THR 8 A THR 8 1_555 A N SEP 9 A SEP 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C SEP 9 A SEP 9 1_555 A N PHE 10 A PHE 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A OD1 ASN 186 A ASN 186 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc2 A OD2 ASP 200 A ASP 200 1_555 E MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc3 A OD2 ASP 200 A ASP 200 1_555 F MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc4 A OD1 ASP 200 A ASP 200 1_555 F MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? metalc ? metalc5 E MG MG . A MG 403 1_555 G O1A ADP . A ADP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc6 E MG MG . A MG 403 1_555 G O1B ADP . A ADP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc7 E MG MG . A MG 403 1_555 J O HOH . A HOH 576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc8 F MG MG . A MG 404 1_555 G O3B ADP . A ADP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc9 F MG MG . A MG 404 1_555 J O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? metalc ? metalc10 F MG MG . A MG 404 1_555 J O HOH . A HOH 562 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? # _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 4NU1 _atom_sites.fract_transf_matrix[1][1] 0.012346 _atom_sites.fract_transf_matrix[1][2] 0.007128 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014256 _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] 0.003565 _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 GOL A 1 401 401 GOL GOL . D 3 GOL A 1 402 402 GOL GOL . E 4 MG A 1 403 403 MG MG . F 4 MG A 1 404 404 MG MG . G 5 ADP A 1 405 405 ADP ADP . H 6 AF3 A 1 406 406 AF3 AF3 . I 7 NO3 A 1 407 407 NO3 NO3 . J 8 HOH A 1 501 501 HOH HOH . J 8 HOH A 2 502 502 HOH HOH . J 8 HOH A 3 503 503 HOH HOH . J 8 HOH A 4 504 504 HOH HOH . J 8 HOH A 5 505 505 HOH HOH . J 8 HOH A 6 506 506 HOH HOH . J 8 HOH A 7 507 507 HOH HOH . J 8 HOH A 8 508 508 HOH HOH . J 8 HOH A 9 509 509 HOH HOH . J 8 HOH A 10 510 510 HOH HOH . J 8 HOH A 11 511 511 HOH HOH . J 8 HOH A 12 512 512 HOH HOH . J 8 HOH A 13 513 513 HOH HOH . J 8 HOH A 14 514 514 HOH HOH . J 8 HOH A 15 515 515 HOH HOH . J 8 HOH A 16 516 516 HOH HOH . J 8 HOH A 17 517 517 HOH HOH . J 8 HOH A 18 518 518 HOH HOH . J 8 HOH A 19 519 519 HOH HOH . J 8 HOH A 20 520 520 HOH HOH . J 8 HOH A 21 521 521 HOH HOH . J 8 HOH A 22 522 522 HOH HOH . J 8 HOH A 23 523 523 HOH HOH . J 8 HOH A 24 524 524 HOH HOH . J 8 HOH A 25 525 525 HOH HOH . J 8 HOH A 26 526 526 HOH HOH . J 8 HOH A 27 527 527 HOH HOH . J 8 HOH A 28 528 528 HOH HOH . J 8 HOH A 29 529 529 HOH HOH . J 8 HOH A 30 530 530 HOH HOH . J 8 HOH A 31 531 531 HOH HOH . J 8 HOH A 32 532 532 HOH HOH . J 8 HOH A 33 533 533 HOH HOH . J 8 HOH A 34 534 534 HOH HOH . J 8 HOH A 35 535 535 HOH HOH . J 8 HOH A 36 536 536 HOH HOH . J 8 HOH A 37 537 537 HOH HOH . J 8 HOH A 38 538 538 HOH HOH . J 8 HOH A 39 539 539 HOH HOH . J 8 HOH A 40 540 540 HOH HOH . J 8 HOH A 41 541 541 HOH HOH . J 8 HOH A 42 542 542 HOH HOH . J 8 HOH A 43 543 543 HOH HOH . J 8 HOH A 44 544 544 HOH HOH . J 8 HOH A 45 545 545 HOH HOH . J 8 HOH A 46 546 546 HOH HOH . J 8 HOH A 47 547 547 HOH HOH . J 8 HOH A 48 548 548 HOH HOH . J 8 HOH A 49 549 549 HOH HOH . J 8 HOH A 50 550 550 HOH HOH . J 8 HOH A 51 551 551 HOH HOH . J 8 HOH A 52 552 552 HOH HOH . J 8 HOH A 53 553 553 HOH HOH . J 8 HOH A 54 554 554 HOH HOH . J 8 HOH A 55 555 555 HOH HOH . J 8 HOH A 56 556 556 HOH HOH . J 8 HOH A 57 557 557 HOH HOH . J 8 HOH A 58 558 558 HOH HOH . J 8 HOH A 59 559 559 HOH HOH . J 8 HOH A 60 560 560 HOH HOH . J 8 HOH A 61 561 561 HOH HOH . J 8 HOH A 62 562 562 HOH HOH . J 8 HOH A 63 563 563 HOH HOH . J 8 HOH A 64 564 564 HOH HOH . J 8 HOH A 65 565 565 HOH HOH . J 8 HOH A 66 566 566 HOH HOH . J 8 HOH A 67 567 567 HOH HOH . J 8 HOH A 68 568 568 HOH HOH . J 8 HOH A 69 569 569 HOH HOH . J 8 HOH A 70 570 570 HOH HOH . J 8 HOH A 71 571 571 HOH HOH . J 8 HOH A 72 572 572 HOH HOH . J 8 HOH A 73 573 573 HOH HOH . J 8 HOH A 74 574 574 HOH HOH . J 8 HOH A 75 575 575 HOH HOH . J 8 HOH A 76 576 576 HOH HOH . J 8 HOH A 77 577 577 HOH HOH . J 8 HOH A 78 578 578 HOH HOH . J 8 HOH A 79 579 579 HOH HOH . J 8 HOH A 80 580 580 HOH HOH . J 8 HOH A 81 581 581 HOH HOH . J 8 HOH A 82 582 582 HOH HOH . J 8 HOH A 83 583 583 HOH HOH . J 8 HOH A 84 584 584 HOH HOH . J 8 HOH A 85 585 585 HOH HOH . J 8 HOH A 86 586 586 HOH HOH . J 8 HOH A 87 587 587 HOH HOH . J 8 HOH A 88 588 588 HOH HOH . J 8 HOH A 89 589 589 HOH HOH . J 8 HOH A 90 590 590 HOH HOH . J 8 HOH A 91 591 591 HOH HOH . J 8 HOH A 92 592 592 HOH HOH . J 8 HOH A 93 593 593 HOH HOH . J 8 HOH A 94 594 594 HOH HOH . K 8 HOH B 1 501 501 HOH HOH . K 8 HOH B 2 502 502 HOH HOH . K 8 HOH B 3 503 503 HOH HOH . K 8 HOH B 4 504 504 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 P PB ADP . . . G 5 -11.222 44.701 -12.4 1 62.26 ? PB ADP 405 A 1 HETATM 2 O O1B ADP . . . G 5 -10.056 44.36 -13.293 1 65.19 ? O1B ADP 405 A 1 HETATM 3 O O2B ADP . . . G 5 -11.542 46.166 -12.516 1 56.58 ? O2B ADP 405 A 1 HETATM 4 O O3B ADP . . . G 5 -12.445 43.926 -12.819 1 54.32 ? O3B ADP 405 A 1 HETATM 5 P PA ADP . . . G 5 -10.212 43.027 -10.395 1 53.27 ? PA ADP 405 A 1 HETATM 6 O O1A ADP . . . G 5 -9.447 42.337 -11.494 1 52.21 ? O1A ADP 405 A 1 HETATM 7 O O2A ADP . . . G 5 -11.267 42.095 -9.851 1 49.27 ? O2A ADP 405 A 1 HETATM 8 O O3A ADP . . . G 5 -10.851 44.372 -10.908 1 81.19 ? O3A ADP 405 A 1 HETATM 9 O O5' ADP . . . G 5 -9.188 43.426 -9.276 1 48.74 ? O5' ADP 405 A 1 HETATM 10 C C5' ADP . . . G 5 -8.255 44.42 -9.623 1 53.71 ? C5' ADP 405 A 1 HETATM 11 C C4' ADP . . . G 5 -6.951 44.107 -9.019 1 57.65 ? C4' ADP 405 A 1 HETATM 12 O O4' ADP . . . G 5 -7.07 44.164 -7.517 1 58.87 ? O4' ADP 405 A 1 HETATM 13 C C3' ADP . . . G 5 -6.534 42.744 -9.392 1 54.89 ? C3' ADP 405 A 1 HETATM 14 O O3' ADP . . . G 5 -5.658 42.752 -10.559 1 54.47 ? O3' ADP 405 A 1 HETATM 15 C C2' ADP . . . G 5 -5.826 42.226 -8.236 1 56.24 ? C2' ADP 405 A 1 HETATM 16 O O2' ADP . . . G 5 -4.397 42.506 -8.358 1 55.45 ? O2' ADP 405 A 1 HETATM 17 C C1' ADP . . . G 5 -6.371 42.914 -7.051 1 57.47 ? C1' ADP 405 A 1 HETATM 18 N N9 ADP . . . G 5 -7.247 42.058 -6.402 1 59.27 ? N9 ADP 405 A 1 HETATM 19 C C8 ADP . . . G 5 -8.448 41.642 -6.811 1 59.33 ? C8 ADP 405 A 1 HETATM 20 N N7 ADP . . . G 5 -8.966 40.821 -5.925 1 60.66 ? N7 ADP 405 A 1 HETATM 21 C C5 ADP . . . G 5 -8.12 40.678 -4.917 1 58.67 ? C5 ADP 405 A 1 HETATM 22 C C6 ADP . . . G 5 -8.135 39.961 -3.745 1 54.2 ? C6 ADP 405 A 1 HETATM 23 N N6 ADP . . . G 5 -9.239 39.153 -3.414 1 51.82 ? N6 ADP 405 A 1 HETATM 24 N N1 ADP . . . G 5 -7.097 40.028 -2.912 1 58.72 ? N1 ADP 405 A 1 HETATM 25 C C2 ADP . . . G 5 -6.034 40.791 -3.197 1 58.98 ? C2 ADP 405 A 1 HETATM 26 N N3 ADP . . . G 5 -5.977 41.502 -4.336 1 58.91 ? N3 ADP 405 A 1 HETATM 27 C C4 ADP . . . G 5 -6.997 41.467 -5.204 1 60.5 ? C4 ADP 405 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #