data_4H81 # _model_server_result.job_id IJVNRKZBqfVpwmzufWMO1Q _model_server_result.datetime_utc '2024-11-14 21:42:25' _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 4h81 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4H81 # _exptl.entry_id 4H81 _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 4H81 _cell.length_a 128.295 _cell.length_b 128.295 _cell.length_c 73.961 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4H81 _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc2 A O VAL 328 A VAL 298 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.87 ? metalc ? metalc3 A O ASP 330 A ASP 300 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? metalc ? metalc4 A O PHE 333 A PHE 303 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc5 A O GLY 367 A GLY 337 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc6 B O1A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc7 B O1B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc8 B O2A ADP . A ADP 401 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.836 ? metalc ? metalc9 C MG MG . A MG 402 1_555 F O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc10 C MG MG . A MG 402 1_555 F O HOH . A HOH 588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc11 C MG MG . A MG 402 1_555 F O HOH . A HOH 593 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? # _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 4H81 _atom_sites.fract_transf_matrix[1][1] 0.007795 _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] 0.007795 _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] 0.013521 _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 WJ2 A 1 404 1 WJ2 WJ2 . 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 24 HOH HOH . F 6 HOH A 24 524 25 HOH HOH . F 6 HOH A 25 525 26 HOH HOH . F 6 HOH A 26 526 27 HOH HOH . F 6 HOH A 27 527 28 HOH HOH . F 6 HOH A 28 528 29 HOH HOH . F 6 HOH A 29 529 31 HOH HOH . F 6 HOH A 30 530 32 HOH HOH . F 6 HOH A 31 531 33 HOH HOH . F 6 HOH A 32 532 34 HOH HOH . F 6 HOH A 33 533 35 HOH HOH . F 6 HOH A 34 534 36 HOH HOH . F 6 HOH A 35 535 37 HOH HOH . F 6 HOH A 36 536 38 HOH HOH . F 6 HOH A 37 537 39 HOH HOH . F 6 HOH A 38 538 40 HOH HOH . F 6 HOH A 39 539 41 HOH HOH . F 6 HOH A 40 540 42 HOH HOH . F 6 HOH A 41 541 43 HOH HOH . F 6 HOH A 42 542 44 HOH HOH . F 6 HOH A 43 543 45 HOH HOH . F 6 HOH A 44 544 46 HOH HOH . F 6 HOH A 45 545 47 HOH HOH . F 6 HOH A 46 546 48 HOH HOH . F 6 HOH A 47 547 49 HOH HOH . F 6 HOH A 48 548 50 HOH HOH . F 6 HOH A 49 549 51 HOH HOH . F 6 HOH A 50 550 53 HOH HOH . F 6 HOH A 51 551 54 HOH HOH . F 6 HOH A 52 552 55 HOH HOH . F 6 HOH A 53 553 56 HOH HOH . F 6 HOH A 54 554 57 HOH HOH . F 6 HOH A 55 555 58 HOH HOH . F 6 HOH A 56 556 59 HOH HOH . F 6 HOH A 57 557 63 HOH HOH . F 6 HOH A 58 558 65 HOH HOH . F 6 HOH A 59 559 66 HOH HOH . F 6 HOH A 60 560 67 HOH HOH . F 6 HOH A 61 561 68 HOH HOH . F 6 HOH A 62 562 69 HOH HOH . F 6 HOH A 63 563 70 HOH HOH . F 6 HOH A 64 564 71 HOH HOH . F 6 HOH A 65 565 72 HOH HOH . F 6 HOH A 66 566 73 HOH HOH . F 6 HOH A 67 567 74 HOH HOH . F 6 HOH A 68 568 75 HOH HOH . F 6 HOH A 69 569 76 HOH HOH . F 6 HOH A 70 570 77 HOH HOH . F 6 HOH A 71 571 83 HOH HOH . F 6 HOH A 72 572 84 HOH HOH . F 6 HOH A 73 573 85 HOH HOH . F 6 HOH A 74 574 86 HOH HOH . F 6 HOH A 75 575 89 HOH HOH . F 6 HOH A 76 576 95 HOH HOH . F 6 HOH A 77 577 96 HOH HOH . F 6 HOH A 78 578 97 HOH HOH . F 6 HOH A 79 579 98 HOH HOH . F 6 HOH A 80 580 99 HOH HOH . F 6 HOH A 81 581 103 HOH HOH . F 6 HOH A 82 582 104 HOH HOH . F 6 HOH A 83 583 105 HOH HOH . F 6 HOH A 84 584 106 HOH HOH . F 6 HOH A 85 585 107 HOH HOH . F 6 HOH A 86 586 113 HOH HOH . F 6 HOH A 87 587 130 HOH HOH . F 6 HOH A 88 588 132 HOH HOH . F 6 HOH A 89 589 133 HOH HOH . F 6 HOH A 90 590 137 HOH HOH . F 6 HOH A 91 591 155 HOH HOH . F 6 HOH A 92 592 159 HOH HOH . F 6 HOH A 93 593 174 HOH HOH . F 6 HOH A 94 594 175 HOH HOH . F 6 HOH A 95 595 179 HOH HOH . F 6 HOH A 96 596 196 HOH HOH . F 6 HOH A 97 597 202 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 4.933 -32.877 -4.784 1 40.85 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 6.234 -33.442 -4.265 1 43.51 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 4.964 -32.564 -6.279 1 43.03 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 3.734 -33.677 -4.312 1 42.38 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 5.667 -30.499 -3.294 1 35.97 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 6.501 -31.14 -2.219 1 35.56 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 4.89 -29.314 -2.855 1 33.67 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 4.61 -31.478 -4.034 1 39.51 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 6.643 -30.051 -4.507 1 39.49 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 6.139 -29.28 -5.591 1 40.09 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 7.094 -29.359 -6.766 1 42.43 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 8.298 -28.664 -6.44 1 38.11 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 7.529 -30.779 -7.086 1 38.12 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 6.573 -31.469 -7.903 1 40.69 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 8.842 -30.542 -7.8 1 41.12 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 8.594 -30.209 -9.175 1 40.45 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 9.375 -29.282 -7.143 1 35.75 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 10.439 -29.576 -6.161 1 37.22 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 10.317 -29.613 -4.813 1 36.95 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 11.517 -29.89 -4.227 1 35.92 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 12.413 -30.031 -5.226 1 33.95 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 13.858 -30.326 -5.313 1 33.39 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 14.574 -30.543 -4.178 1 29.8 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 14.408 -30.384 -6.548 1 32.16 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 13.684 -30.19 -7.67 1 35.58 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 12.368 -29.916 -7.674 1 38.88 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 11.703 -29.821 -6.493 1 34.31 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #