data_5KPZ # _model_server_result.job_id o51G6xgGLHqPhuxa3zCWyg _model_server_result.datetime_utc '2024-10-11 11:18:29' _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 5kpz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5KPZ # _exptl.entry_id 5KPZ _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 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 5KPZ _cell.length_a 99.488 _cell.length_b 99.488 _cell.length_c 68.542 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KPZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -22.847333 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 B O7 PAZ . A PAZ 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc2 C O2B ADP . A ADP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc3 D MG MG . A MG 403 1_555 E O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc4 D MG MG . A MG 403 1_555 E O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? metalc ? metalc5 D MG MG . A MG 403 1_555 E O HOH . A HOH 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc6 D MG MG . A MG 403 1_555 E O HOH . A HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? # _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 5KPZ _atom_sites.fract_transf_matrix[1][1] 0.010051 _atom_sites.fract_transf_matrix[1][2] 0.005803 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011606 _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] 0.01459 _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 PAZ A 1 401 1 PAZ PAZ . C 3 ADP A 1 402 1 ADP ADP . D 4 MG A 1 403 1 MG MG . E 5 HOH A 1 501 2 HOH HOH . E 5 HOH A 2 502 7 HOH HOH . E 5 HOH A 3 503 24 HOH HOH . E 5 HOH A 4 504 40 HOH HOH . E 5 HOH A 5 505 21 HOH HOH . E 5 HOH A 6 506 42 HOH HOH . E 5 HOH A 7 507 18 HOH HOH . E 5 HOH A 8 508 4 HOH HOH . E 5 HOH A 9 509 38 HOH HOH . E 5 HOH A 10 510 16 HOH HOH . E 5 HOH A 11 511 26 HOH HOH . E 5 HOH A 12 512 10 HOH HOH . E 5 HOH A 13 513 1 HOH HOH . E 5 HOH A 14 514 45 HOH HOH . E 5 HOH A 15 515 5 HOH HOH . E 5 HOH A 16 516 46 HOH HOH . E 5 HOH A 17 517 20 HOH HOH . E 5 HOH A 18 518 6 HOH HOH . E 5 HOH A 19 519 3 HOH HOH . E 5 HOH A 20 520 8 HOH HOH . E 5 HOH A 21 521 36 HOH HOH . E 5 HOH A 22 522 30 HOH HOH . E 5 HOH A 23 523 37 HOH HOH . E 5 HOH A 24 524 11 HOH HOH . E 5 HOH A 25 525 50 HOH HOH . E 5 HOH A 26 526 52 HOH HOH . E 5 HOH A 27 527 48 HOH HOH . E 5 HOH A 28 528 29 HOH HOH . E 5 HOH A 29 529 41 HOH HOH . E 5 HOH A 30 530 31 HOH HOH . E 5 HOH A 31 531 28 HOH HOH . E 5 HOH A 32 532 32 HOH HOH . E 5 HOH A 33 533 43 HOH HOH . E 5 HOH A 34 534 34 HOH HOH . E 5 HOH A 35 535 44 HOH HOH . E 5 HOH A 36 536 33 HOH HOH . E 5 HOH A 37 537 51 HOH HOH . E 5 HOH A 38 538 27 HOH HOH . E 5 HOH A 39 539 54 HOH HOH . E 5 HOH A 40 540 17 HOH HOH . E 5 HOH A 41 541 53 HOH HOH . E 5 HOH A 42 542 39 HOH HOH . E 5 HOH A 43 543 13 HOH HOH . E 5 HOH A 44 544 35 HOH HOH . E 5 HOH A 45 545 19 HOH HOH . E 5 HOH A 46 546 22 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 . . . C 3 27.039 13.725 0.58 1 40.76 ? PB ADP 402 A 1 HETATM 2 O O1B ADP . . . C 3 27.019 13.658 -0.878 1 43.71 ? O1B ADP 402 A 1 HETATM 3 O O2B ADP . . . C 3 28.377 14.332 1.053 1 46.05 ? O2B ADP 402 A 1 HETATM 4 O O3B ADP . . . C 3 25.848 14.477 1.073 1 43.19 ? O3B ADP 402 A 1 HETATM 5 P PA ADP . . . C 3 27.074 11.57 2.444 1 37.66 ? PA ADP 402 A 1 HETATM 6 O O1A ADP . . . C 3 28.505 11.202 2.727 1 42.51 ? O1A ADP 402 A 1 HETATM 7 O O2A ADP . . . C 3 26.477 12.496 3.523 1 38.26 ? O2A ADP 402 A 1 HETATM 8 O O3A ADP . . . C 3 26.878 12.215 1.025 1 37.64 ? O3A ADP 402 A 1 HETATM 9 O O5' ADP . . . C 3 26.278 10.246 2.257 1 37.43 ? O5' ADP 402 A 1 HETATM 10 C C5' ADP . . . C 3 25.149 10.312 1.404 1 37.29 ? C5' ADP 402 A 1 HETATM 11 C C4' ADP . . . C 3 24.598 8.924 1.365 1 38.31 ? C4' ADP 402 A 1 HETATM 12 O O4' ADP . . . C 3 24.481 8.416 2.577 1 38.23 ? O4' ADP 402 A 1 HETATM 13 C C3' ADP . . . C 3 23.209 8.88 0.738 1 39.61 ? C3' ADP 402 A 1 HETATM 14 O O3' ADP . . . C 3 23.401 8.644 -0.553 1 37.32 ? O3' ADP 402 A 1 HETATM 15 C C2' ADP . . . C 3 22.593 7.606 1.401 1 40.4 ? C2' ADP 402 A 1 HETATM 16 O O2' ADP . . . C 3 22.974 6.441 0.557 1 37.65 ? O2' ADP 402 A 1 HETATM 17 C C1' ADP . . . C 3 23.168 7.468 2.555 1 41.6 ? C1' ADP 402 A 1 HETATM 18 N N9 ADP . . . C 3 22.403 7.843 3.668 1 42.63 ? N9 ADP 402 A 1 HETATM 19 C C8 ADP . . . C 3 22.652 7.37 4.919 1 42.6 ? C8 ADP 402 A 1 HETATM 20 N N7 ADP . . . C 3 21.782 7.915 5.752 1 43.44 ? N7 ADP 402 A 1 HETATM 21 C C5 ADP . . . C 3 20.973 8.746 5.024 1 43.52 ? C5 ADP 402 A 1 HETATM 22 C C6 ADP . . . C 3 19.907 9.554 5.424 1 39.17 ? C6 ADP 402 A 1 HETATM 23 N N6 ADP . . . C 3 19.357 9.738 6.706 1 40.68 ? N6 ADP 402 A 1 HETATM 24 N N1 ADP . . . C 3 19.246 10.315 4.522 1 39.15 ? N1 ADP 402 A 1 HETATM 25 C C2 ADP . . . C 3 19.624 10.261 3.242 1 42.96 ? C2 ADP 402 A 1 HETATM 26 N N3 ADP . . . C 3 20.679 9.468 2.845 1 37.98 ? N3 ADP 402 A 1 HETATM 27 C C4 ADP . . . C 3 21.361 8.712 3.745 1 40.1 ? C4 ADP 402 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #