data_4H85 # _model_server_result.job_id 53LO6_kHUvFEDHnCA2Txrw _model_server_result.datetime_utc '2024-12-02 22:40:31' _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 4h85 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4H85 # _exptl.entry_id 4H85 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 90 _cell.entry_id 4H85 _cell.length_a 127.619 _cell.length_b 127.619 _cell.length_c 73.987 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4H85 _symmetry.cell_setting ? _symmetry.Int_Tables_number 94 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 42 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 A OD1 ASN 279 A ASN 249 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc2 A O VAL 328 A VAL 298 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc3 A O ASP 330 A ASP 300 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.82 ? metalc ? metalc4 A O PHE 333 A PHE 303 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.889 ? metalc ? metalc5 A O GLY 367 A GLY 337 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc6 B O1A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc7 B O1B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc8 B O2A ADP . A ADP 401 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc9 C MG MG . A MG 402 1_555 F O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc10 C MG MG . A MG 402 1_555 F O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc11 C MG MG . A MG 402 1_555 F O HOH . A HOH 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? # _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 4H85 _atom_sites.fract_transf_matrix[1][1] 0.007836 _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] 0.007836 _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] 0.013516 _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 B 2 ADP A 1 401 1 ADP ADP . C 3 MG A 1 402 1 MG MG . D 4 K A 1 403 1 K K . E 5 HRI A 1 404 1 HRI HRI . F 6 HOH A 1 501 1 HOH HOH . F 6 HOH A 2 502 2 HOH HOH . F 6 HOH A 3 503 3 HOH HOH . F 6 HOH A 4 504 4 HOH HOH . F 6 HOH A 5 505 5 HOH HOH . F 6 HOH A 6 506 6 HOH HOH . F 6 HOH A 7 507 7 HOH HOH . F 6 HOH A 8 508 8 HOH HOH . F 6 HOH A 9 509 9 HOH HOH . F 6 HOH A 10 510 10 HOH HOH . F 6 HOH A 11 511 11 HOH HOH . F 6 HOH A 12 512 12 HOH HOH . F 6 HOH A 13 513 13 HOH HOH . F 6 HOH A 14 514 14 HOH HOH . F 6 HOH A 15 515 15 HOH HOH . F 6 HOH A 16 516 16 HOH HOH . F 6 HOH A 17 517 17 HOH HOH . F 6 HOH A 18 518 18 HOH HOH . F 6 HOH A 19 519 19 HOH HOH . F 6 HOH A 20 520 20 HOH HOH . F 6 HOH A 21 521 21 HOH HOH . F 6 HOH A 22 522 22 HOH HOH . F 6 HOH A 23 523 23 HOH HOH . F 6 HOH A 24 524 27 HOH HOH . F 6 HOH A 25 525 30 HOH HOH . F 6 HOH A 26 526 31 HOH HOH . F 6 HOH A 27 527 32 HOH HOH . F 6 HOH A 28 528 33 HOH HOH . F 6 HOH A 29 529 35 HOH HOH . F 6 HOH A 30 530 36 HOH HOH . F 6 HOH A 31 531 37 HOH HOH . F 6 HOH A 32 532 38 HOH HOH . F 6 HOH A 33 533 39 HOH HOH . F 6 HOH A 34 534 40 HOH HOH . F 6 HOH A 35 535 41 HOH HOH . F 6 HOH A 36 536 42 HOH HOH . F 6 HOH A 37 537 43 HOH HOH . F 6 HOH A 38 538 44 HOH HOH . F 6 HOH A 39 539 45 HOH HOH . F 6 HOH A 40 540 46 HOH HOH . F 6 HOH A 41 541 47 HOH HOH . F 6 HOH A 42 542 48 HOH HOH . F 6 HOH A 43 543 49 HOH HOH . F 6 HOH A 44 544 50 HOH HOH . F 6 HOH A 45 545 51 HOH HOH . F 6 HOH A 46 546 52 HOH HOH . F 6 HOH A 47 547 53 HOH HOH . F 6 HOH A 48 548 54 HOH HOH . F 6 HOH A 49 549 55 HOH HOH . F 6 HOH A 50 550 56 HOH HOH . F 6 HOH A 51 551 58 HOH HOH . F 6 HOH A 52 552 59 HOH HOH . F 6 HOH A 53 553 60 HOH HOH . F 6 HOH A 54 554 61 HOH HOH . F 6 HOH A 55 555 62 HOH HOH . F 6 HOH A 56 556 68 HOH HOH . F 6 HOH A 57 557 71 HOH HOH . F 6 HOH A 58 558 72 HOH HOH . F 6 HOH A 59 559 74 HOH HOH . F 6 HOH A 60 560 77 HOH HOH . F 6 HOH A 61 561 79 HOH HOH . F 6 HOH A 62 562 83 HOH HOH . F 6 HOH A 63 563 84 HOH HOH . F 6 HOH A 64 564 85 HOH HOH . F 6 HOH A 65 565 86 HOH HOH . F 6 HOH A 66 566 87 HOH HOH . F 6 HOH A 67 567 88 HOH HOH . F 6 HOH A 68 568 89 HOH HOH . F 6 HOH A 69 569 92 HOH HOH . F 6 HOH A 70 570 93 HOH HOH . F 6 HOH A 71 571 94 HOH HOH . F 6 HOH A 72 572 96 HOH HOH . F 6 HOH A 73 573 98 HOH HOH . F 6 HOH A 74 574 99 HOH HOH . F 6 HOH A 75 575 101 HOH HOH . F 6 HOH A 76 576 103 HOH HOH . F 6 HOH A 77 577 107 HOH HOH . F 6 HOH A 78 578 108 HOH HOH . F 6 HOH A 79 579 110 HOH HOH . F 6 HOH A 80 580 112 HOH HOH . F 6 HOH A 81 581 113 HOH HOH . F 6 HOH A 82 582 115 HOH HOH . F 6 HOH A 83 583 116 HOH HOH . F 6 HOH A 84 584 117 HOH HOH . F 6 HOH A 85 585 121 HOH HOH . F 6 HOH A 86 586 123 HOH HOH . F 6 HOH A 87 587 125 HOH HOH . F 6 HOH A 88 588 126 HOH HOH . F 6 HOH A 89 589 127 HOH HOH . F 6 HOH A 90 590 128 HOH HOH . F 6 HOH A 91 591 130 HOH HOH . F 6 HOH A 92 592 134 HOH HOH . F 6 HOH A 93 593 139 HOH HOH . F 6 HOH A 94 594 142 HOH HOH . F 6 HOH A 95 595 143 HOH HOH . F 6 HOH A 96 596 152 HOH HOH . F 6 HOH A 97 597 153 HOH HOH . F 6 HOH A 98 598 154 HOH HOH . F 6 HOH A 99 599 155 HOH HOH . F 6 HOH A 100 600 159 HOH HOH . F 6 HOH A 101 601 161 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 . . . B 2 4.757 -32.729 -4.648 1 39.67 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 6.042 -33.32 -4.13 1 42.31 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 4.818 -32.404 -6.14 1 42.61 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 3.549 -33.5 -4.172 1 38.21 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 5.508 -30.331 -3.175 1 35.7 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 6.307 -30.983 -2.084 1 39.21 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 4.719 -29.151 -2.751 1 31.32 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 4.446 -31.318 -3.913 1 39.84 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 6.486 -29.905 -4.386 1 37.6 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 5.947 -29.186 -5.49 1 40.98 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 6.876 -29.255 -6.688 1 41.71 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 8.082 -28.55 -6.38 1 37.66 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 7.305 -30.677 -7.016 1 38.08 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 6.361 -31.352 -7.865 1 40.8 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 8.617 -30.432 -7.718 1 39.75 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 8.342 -30.101 -9.085 1 39.5 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 9.157 -29.155 -7.085 1 37.29 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 10.229 -29.419 -6.096 1 38.96 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 10.106 -29.437 -4.748 1 38.31 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 11.303 -29.697 -4.158 1 33.94 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 12.197 -29.845 -5.153 1 34.6 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 13.645 -30.133 -5.231 1 32.65 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 14.36 -30.314 -4.093 1 30.9 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 14.2 -30.211 -6.458 1 33.69 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 13.48 -30.028 -7.588 1 34.08 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 12.162 -29.772 -7.596 1 38.73 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 11.491 -29.661 -6.42 1 32.29 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 1028 _model_server_stats.encode_time_ms 61 _model_server_stats.element_count 27 #