data_8F4Q # _model_server_result.job_id cSsw_hx6dIyFOEQ2TOkRAA _model_server_result.datetime_utc '2025-01-10 10:39:49' _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 8f4q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8F4Q # _exptl.entry_id 8F4Q _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 120 _cell.entry_id 8F4Q _cell.length_a 111.67 _cell.length_b 111.67 _cell.length_c 139.34 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8F4Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 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 _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' 4_765 -x+2,-y+1,z -1 0 0 0 -1 0 0 0 1 167.505 96.709057 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 # _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 8F4Q _atom_sites.fract_transf_matrix[1][1] 0.008955 _atom_sites.fract_transf_matrix[1][2] 0.00517 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01034 _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] 0.007177 _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 1 401 401 ADP ADP . C 3 SO4 A 1 402 404 SO4 SO4 . D 3 SO4 A 1 403 405 SO4 SO4 . E 4 XER A 1 404 501 XER PFE . F 4 XER A 1 405 601 XER PFE . G 4 XER A 1 406 701 XER PFE . H 5 HOH A 1 501 55 HOH HOH . H 5 HOH A 2 502 24 HOH HOH . H 5 HOH A 3 503 69 HOH HOH . H 5 HOH A 4 504 79 HOH HOH . H 5 HOH A 5 505 21 HOH HOH . H 5 HOH A 6 506 76 HOH HOH . H 5 HOH A 7 507 78 HOH HOH . H 5 HOH A 8 508 58 HOH HOH . H 5 HOH A 9 509 6 HOH HOH . H 5 HOH A 10 510 61 HOH HOH . H 5 HOH A 11 511 70 HOH HOH . H 5 HOH A 12 512 54 HOH HOH . H 5 HOH A 13 513 12 HOH HOH . H 5 HOH A 14 514 60 HOH HOH . H 5 HOH A 15 515 30 HOH HOH . H 5 HOH A 16 516 57 HOH HOH . H 5 HOH A 17 517 40 HOH HOH . H 5 HOH A 18 518 4 HOH HOH . H 5 HOH A 19 519 81 HOH HOH . H 5 HOH A 20 520 25 HOH HOH . H 5 HOH A 21 521 46 HOH HOH . H 5 HOH A 22 522 65 HOH HOH . H 5 HOH A 23 523 80 HOH HOH . H 5 HOH A 24 524 33 HOH HOH . H 5 HOH A 25 525 39 HOH HOH . H 5 HOH A 26 526 49 HOH HOH . H 5 HOH A 27 527 59 HOH HOH . H 5 HOH A 28 528 63 HOH HOH . H 5 HOH A 29 529 62 HOH HOH . H 5 HOH A 30 530 26 HOH HOH . H 5 HOH A 31 531 82 HOH HOH . H 5 HOH A 32 532 36 HOH HOH . H 5 HOH A 33 533 15 HOH HOH . H 5 HOH A 34 534 18 HOH HOH . H 5 HOH A 35 535 44 HOH HOH . H 5 HOH A 36 536 41 HOH HOH . H 5 HOH A 37 537 22 HOH HOH . H 5 HOH A 38 538 11 HOH HOH . H 5 HOH A 39 539 27 HOH HOH . H 5 HOH A 40 540 17 HOH HOH . H 5 HOH A 41 541 34 HOH HOH . H 5 HOH A 42 542 29 HOH HOH . H 5 HOH A 43 543 23 HOH HOH . H 5 HOH A 44 544 47 HOH HOH . H 5 HOH A 45 545 71 HOH HOH . H 5 HOH A 46 546 42 HOH HOH . H 5 HOH A 47 547 67 HOH HOH . H 5 HOH A 48 548 66 HOH HOH . H 5 HOH A 49 549 50 HOH HOH . H 5 HOH A 50 550 16 HOH HOH . H 5 HOH A 51 551 13 HOH HOH . H 5 HOH A 52 552 28 HOH HOH . H 5 HOH A 53 553 68 HOH HOH . H 5 HOH A 54 554 48 HOH HOH . H 5 HOH A 55 555 83 HOH HOH . H 5 HOH A 56 556 31 HOH HOH . H 5 HOH A 57 557 37 HOH HOH . H 5 HOH A 58 558 73 HOH HOH . H 5 HOH A 59 559 45 HOH HOH . H 5 HOH A 60 560 38 HOH HOH . H 5 HOH A 61 561 52 HOH HOH . H 5 HOH A 62 562 77 HOH HOH . H 5 HOH A 63 563 20 HOH HOH . H 5 HOH A 64 564 74 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 89.27 28.898 18.797 1 87.7 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 89.934 29.455 17.552 1 87.46 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 90 27.691 19.354 1 88.04 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 87.786 28.655 18.619 1 87.9 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 89.139 31.605 20.2 1 85.4 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 89.995 32.367 19.263 1 85.63 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 89.219 31.871 21.66 1 85.29 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 89.401 30.041 19.967 1 86.75 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 87.633 31.803 19.677 1 83.42 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 86.479 31.521 20.501 1 81.56 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 85.229 31.53 19.653 1 79.9 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 84.873 32.882 19.277 1 78.9 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 85.313 30.797 18.324 1 79.26 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 85.269 29.38 18.463 1 79.44 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 84.115 31.388 17.575 1 78.64 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 82.884 30.793 17.985 1 79.08 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 84.132 32.848 18.062 1 77.31 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 84.689 33.811 17.111 1 74.15 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 85.861 34.516 17.204 1 73.35 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 86.078 35.332 16.201 1 72.68 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 84.969 35.152 15.386 1 72.31 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 84.568 35.755 14.176 1 70.84 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 85.335 36.578 13.468 1 69.88 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 83.374 35.398 13.662 1 71.36 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 82.641 34.481 14.304 1 71.7 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 82.917 33.836 15.438 1 72.49 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 84.104 34.217 15.934 1 73.11 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 677 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #