data_4V81 # _model_server_result.job_id zCem9sS-TON7DgVVldjrdQ _model_server_result.datetime_utc '2025-01-03 04:42:41' _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 4v81 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"HB","auth_seq_id":601}' # _entry.id 4V81 # _exptl.entry_id 4V81 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 9 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 24 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 85.23 _cell.angle_beta 81.15 _cell.angle_gamma 61.17 _cell.entry_id 4V81 _cell.length_a 159.1 _cell.length_b 162.54 _cell.length_c 268.1 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4V81 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexadecameric 16 author_and_software_defined_assembly 1 PISA hexadecameric 16 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,KC,LC,MC,NC 1 1 Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,JB,KB,LB,MB,NB,OB,PB,QB,RB,SB,TB,UB,VB,WB,XB,YB,ZB,AC,BC,CC,DC,EC,FC,GC,HC,IC,JC,OC,PC,QC 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 9 GA N N ? 9 IA N N ? 9 KA N N ? 9 MA N N ? 9 OA N N ? 9 QA N N ? 9 SA N N ? 9 UA N N ? 9 XA N N ? 9 AB N N ? 9 CB N N ? 9 EB N N ? 9 HB N N ? 9 JB N N ? 9 LB N N ? 9 PB N N ? 9 RB N N ? 9 TB N N ? 9 VB N N ? 9 ZB N N ? 9 BC N N ? 9 DC N N ? 9 FC N N ? 9 IC N 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 GA O1B ADP . A ADP 601 1_555 HA BE BEF . A BEF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? metalc ? metalc2 IA O1B ADP . B ADP 601 1_555 JA BE BEF . B BEF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? metalc ? metalc3 OA O1B ADP . E ADP 601 1_555 PA BE BEF . E BEF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? metalc ? metalc4 XA O1B ADP . J ADP 601 1_555 YA BE BEF . J BEF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? metalc ? metalc5 EB O1B ADP . N ADP 601 1_555 FB BE BEF . N BEF 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? metalc ? metalc6 LB O1B ADP . b ADP 1601 1_555 MB BE BEF . b BEF 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 ? metalc ? metalc7 VB O1B ADP . h ADP 1601 1_555 WB BE BEF . h BEF 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? metalc ? metalc8 ZB O1B ADP . k ADP 2101 1_555 AC BE BEF . k BEF 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? metalc ? metalc9 BC O1B ADP . l ADP 1601 1_555 CC BE BEF . l BEF 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.411 ? metalc ? metalc10 IC O1B ADP . p ADP 1601 1_555 JC BE BEF . p BEF 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? # _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 4V81 _atom_sites.fract_transf_matrix[1][1] 0.006285 _atom_sites.fract_transf_matrix[1][2] -0.00346 _atom_sites.fract_transf_matrix[1][3] -0.000943 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007023 _atom_sites.fract_transf_matrix[2][3] -0.000073 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.003775 _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 GA 9 ADP A 1 601 756 ADP ADP . HA 10 BEF A 1 602 757 BEF BEF . IA 9 ADP B 1 601 756 ADP ADP . JA 10 BEF B 1 602 757 BEF BEF . KA 9 ADP C 1 1101 756 ADP ADP . LA 10 BEF C 1 1102 757 BEF BEF . MA 9 ADP D 1 601 756 ADP ADP . NA 10 BEF D 1 602 757 BEF BEF . OA 9 ADP E 1 601 756 ADP ADP . PA 10 BEF E 1 602 757 BEF BEF . QA 9 ADP F 1 601 756 ADP ADP . RA 10 BEF F 1 602 757 BEF BEF . SA 9 ADP G 1 601 756 ADP ADP . TA 10 BEF G 1 602 757 BEF BEF . UA 9 ADP H 1 601 756 ADP ADP . VA 10 BEF H 1 602 757 BEF BEF . WA 11 SO4 I 1 600 600 SO4 SO4 . XA 9 ADP J 1 601 756 ADP ADP . YA 10 BEF J 1 602 757 BEF BEF . ZA 11 SO4 K 1 1101 600 SO4 SO4 . AB 9 ADP L 1 601 756 ADP ADP . BB 10 BEF L 1 602 757 BEF BEF . CB 9 ADP M 1 601 756 ADP ADP . DB 10 BEF M 1 602 757 BEF BEF . EB 9 ADP N 1 601 756 ADP ADP . FB 10 BEF N 1 602 757 BEF BEF . GB 11 SO4 O 1 600 600 SO4 SO4 . HB 9 ADP P 1 601 756 ADP ADP . IB 10 BEF P 1 602 757 BEF BEF . JB 9 ADP a 1 1601 1756 ADP ADP . KB 10 BEF a 1 1602 1757 BEF BEF . LB 9 ADP b 1 1601 1756 ADP ADP . MB 10 BEF b 1 1602 1757 BEF BEF . NB 11 SO4 c 1 2101 1600 SO4 SO4 . OB 11 SO4 d 1 1600 1600 SO4 SO4 . PB 9 ADP e 1 1601 1756 ADP ADP . QB 10 BEF e 1 1602 1757 BEF BEF . RB 9 ADP f 1 1601 1756 ADP ADP . SB 10 BEF f 1 1602 1757 BEF BEF . TB 9 ADP g 1 1601 1756 ADP ADP . UB 10 BEF g 1 1602 1757 BEF BEF . VB 9 ADP h 1 1601 1756 ADP ADP . WB 10 BEF h 1 1602 1757 BEF BEF . XB 11 SO4 i 1 1600 1600 SO4 SO4 . YB 11 SO4 j 1 1600 1600 SO4 SO4 . ZB 9 ADP k 1 2101 1756 ADP ADP . AC 10 BEF k 1 2102 1757 BEF BEF . BC 9 ADP l 1 1601 1756 ADP ADP . CC 10 BEF l 1 1602 1757 BEF BEF . DC 9 ADP m 1 1601 1756 ADP ADP . EC 10 BEF m 1 1602 1757 BEF BEF . FC 9 ADP n 1 1601 1756 ADP ADP . GC 10 BEF n 1 1602 1757 BEF BEF . HC 11 SO4 o 1 1600 1600 SO4 SO4 . IC 9 ADP p 1 1601 1756 ADP ADP . JC 10 BEF p 1 1602 1757 BEF BEF . KC 12 HOH B 1 800 800 HOH HOH . LC 12 HOH E 1 800 800 HOH HOH . MC 12 HOH G 1 800 800 HOH HOH . NC 12 HOH M 1 800 800 HOH HOH . OC 12 HOH e 1 1800 1800 HOH HOH . PC 12 HOH g 1 1800 1800 HOH HOH . QC 12 HOH m 1 1800 1800 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 . . . HB 9 138.99 15.106 180.296 1 151.61 ? PB ADP 601 P 1 HETATM 2 O O1B ADP . . . HB 9 140.244 15.159 179.237 1 152.57 ? O1B ADP 601 P 1 HETATM 3 O O2B ADP . . . HB 9 138.334 16.609 180.446 1 119.65 ? O2B ADP 601 P 1 HETATM 4 O O3B ADP . . . HB 9 139.482 14.663 181.599 1 154.35 ? O3B ADP 601 P 1 HETATM 5 P PA ADP . . . HB 9 138.282 12.855 178.738 1 108.22 ? PA ADP 601 P 1 HETATM 6 O O1A ADP . . . HB 9 137.774 13.183 177.204 1 124.97 ? O1A ADP 601 P 1 HETATM 7 O O2A ADP . . . HB 9 139.741 12.761 178.774 1 106.9 ? O2A ADP 601 P 1 HETATM 8 O O3A ADP . . . HB 9 137.832 14.062 179.759 1 73.04 ? O3A ADP 601 P 1 HETATM 9 O O5' ADP . . . HB 9 137.644 11.429 179.246 1 159.34 ? O5' ADP 601 P 1 HETATM 10 C C5' ADP . . . HB 9 137.747 11.107 180.598 1 161.38 ? C5' ADP 601 P 1 HETATM 11 C C4' ADP . . . HB 9 138.478 9.818 180.962 1 160.92 ? C4' ADP 601 P 1 HETATM 12 O O4' ADP . . . HB 9 138.042 8.585 180.306 1 159.11 ? O4' ADP 601 P 1 HETATM 13 C C3' ADP . . . HB 9 138.428 9.351 182.437 1 161.22 ? C3' ADP 601 P 1 HETATM 14 O O3' ADP . . . HB 9 138.803 10.231 183.467 1 157.54 ? O3' ADP 601 P 1 HETATM 15 C C2' ADP . . . HB 9 137.071 8.681 182.473 1 162.77 ? C2' ADP 601 P 1 HETATM 16 O O2' ADP . . . HB 9 135.965 9.414 182.925 1 164.95 ? O2' ADP 601 P 1 HETATM 17 C C1' ADP . . . HB 9 137.01 8.029 181.124 1 158.98 ? C1' ADP 601 P 1 HETATM 18 N N9 ADP . . . HB 9 137.202 6.601 181.274 1 153.95 ? N9 ADP 601 P 1 HETATM 19 C C8 ADP . . . HB 9 136.253 5.697 181.438 1 154.91 ? C8 ADP 601 P 1 HETATM 20 N N7 ADP . . . HB 9 136.852 4.456 181.563 1 152.15 ? N7 ADP 601 P 1 HETATM 21 C C5 ADP . . . HB 9 138.199 4.639 181.472 1 150.72 ? C5 ADP 601 P 1 HETATM 22 C C6 ADP . . . HB 9 139.235 3.76 181.532 1 155.21 ? C6 ADP 601 P 1 HETATM 23 N N6 ADP . . . HB 9 138.962 2.349 181.741 1 153.65 ? N6 ADP 601 P 1 HETATM 24 N N1 ADP . . . HB 9 140.482 4.204 181.412 1 159.74 ? N1 ADP 601 P 1 HETATM 25 C C2 ADP . . . HB 9 140.724 5.523 181.232 1 154.53 ? C2 ADP 601 P 1 HETATM 26 N N3 ADP . . . HB 9 139.692 6.398 181.173 1 147.28 ? N3 ADP 601 P 1 HETATM 27 C C4 ADP . . . HB 9 138.439 5.949 181.293 1 148.71 ? C4 ADP 601 P 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 565 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #