data_7VYI # _model_server_result.job_id z-EjU9U4t0UOK3W83NEFXA _model_server_result.datetime_utc '2024-12-21 17:03:46' _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 7vyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"XA","auth_seq_id":401}' # _entry.id 7VYI # _exptl.entry_id 7VYI _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 35 _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 7VYI _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7VYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details 29-meric _pdbx_struct_assembly.oligomeric_count 29 _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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? _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 # _struct_asym.details ? _struct_asym.entity_id 35 _struct_asym.id XA _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 disulf ? disulf1 D SG CYS 94 V CYS 95 1_555 D SG CYS 114 V CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf2 L SG CYS 112 d CYS 113 1_555 L SG CYS 124 d CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 P SG CYS 32 h CYS 33 1_555 P SG CYS 65 h CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 P SG CYS 42 h CYS 43 1_555 P SG CYS 55 h CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 AA SG CYS 87 u CYS 88 1_555 AA SG CYS 99 u CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 BA SG CYS 69 v CYS 69 1_555 BA SG CYS 80 v CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _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 ? # _atom_sites.entry_id 7VYI _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 DA 30 PEE U 1 101 101 PEE PEE . EA 30 PEE U 1 102 401 PEE PEE . FA 31 8Q1 X 1 201 201 8Q1 8Q1 . GA 32 CDL a 1 201 201 CDL CDL . HA 33 PLX a 1 202 101 PLX PLX . IA 30 PEE b 1 201 720 PEE PEE . JA 33 PLX g 1 201 705 PLX PLX . KA 32 CDL g 1 202 102 CDL CDL . LA 32 CDL i 1 401 401 CDL CDL . MA 30 PEE i 1 402 718 PEE PEE . NA 33 PLX j 1 201 203 PLX PLX . OA 32 CDL l 1 701 713 CDL CDL . PA 30 PEE l 1 702 719 PEE PEE . QA 30 PEE m 1 201 202 PEE PEE . RA 30 PEE r 1 501 202 PEE PEE . SA 33 PLX r 1 502 205 PLX PLX . TA 33 PLX r 1 503 201 PLX PLX . UA 32 CDL r 1 504 712 CDL CDL . VA 32 CDL r 1 505 714 CDL CDL . WA 34 UQ s 1 401 403 UQ UQ . XA 35 ADP w 1 401 401 ADP ADP . # 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 . . . XA 35 194.688 138.804 173.566 0.5 57.54 ? PB ADP 401 w 1 HETATM 2 O O1B ADP . . . XA 35 193.716 138.08 172.683 0.5 57.54 ? O1B ADP 401 w 1 HETATM 3 O O2B ADP . . . XA 35 195.001 137.944 174.785 0.5 57.54 ? O2B ADP 401 w 1 HETATM 4 O O3B ADP . . . XA 35 195.955 139.07 172.8 0.5 57.54 ? O3B ADP 401 w 1 HETATM 5 P PA ADP . . . XA 35 193.053 141.176 173.116 0.5 57.54 ? PA ADP 401 w 1 HETATM 6 O O1A ADP . . . XA 35 191.995 140.329 172.471 0.5 57.54 ? O1A ADP 401 w 1 HETATM 7 O O2A ADP . . . XA 35 192.389 142.222 173.972 0.5 57.54 ? O2A ADP 401 w 1 HETATM 8 O O3A ADP . . . XA 35 194.035 140.227 174.06 0.5 57.54 ? O3A ADP 401 w 1 HETATM 9 O O5' ADP . . . XA 35 193.953 141.922 171.955 0.5 57.54 ? O5' ADP 401 w 1 HETATM 10 C C5' ADP . . . XA 35 195.284 142.27 172.265 0.5 57.54 ? C5' ADP 401 w 1 HETATM 11 C C4' ADP . . . XA 35 195.415 143.803 172.211 0.5 57.54 ? C4' ADP 401 w 1 HETATM 12 O O4' ADP . . . XA 35 194.696 144.376 170.879 0.5 57.54 ? O4' ADP 401 w 1 HETATM 13 C C3' ADP . . . XA 35 194.826 144.334 173.24 0.5 57.54 ? C3' ADP 401 w 1 HETATM 14 O O3' ADP . . . XA 35 195.768 145.261 173.947 0.5 57.54 ? O3' ADP 401 w 1 HETATM 15 C C2' ADP . . . XA 35 193.615 145.129 172.679 0.5 57.54 ? C2' ADP 401 w 1 HETATM 16 O O2' ADP . . . XA 35 193.431 146.264 173.379 0.5 57.54 ? O2' ADP 401 w 1 HETATM 17 C C1' ADP . . . XA 35 194.043 145.45 171.254 0.5 57.54 ? C1' ADP 401 w 1 HETATM 18 N N9 ADP . . . XA 35 192.854 145.686 170.372 0.5 57.54 ? N9 ADP 401 w 1 HETATM 19 C C8 ADP . . . XA 35 192.245 144.774 169.648 0.5 57.54 ? C8 ADP 401 w 1 HETATM 20 N N7 ADP . . . XA 35 191.231 145.346 168.991 0.5 57.54 ? N7 ADP 401 w 1 HETATM 21 C C5 ADP . . . XA 35 191.202 146.651 169.307 0.5 57.54 ? C5 ADP 401 w 1 HETATM 22 C C6 ADP . . . XA 35 190.368 147.744 168.925 0.5 57.54 ? C6 ADP 401 w 1 HETATM 23 N N6 ADP . . . XA 35 189.246 147.552 167.983 0.5 57.54 ? N6 ADP 401 w 1 HETATM 24 N N1 ADP . . . XA 35 190.629 148.943 169.445 0.5 57.54 ? N1 ADP 401 w 1 HETATM 25 C C2 ADP . . . XA 35 191.632 149.131 170.293 0.5 57.54 ? C2 ADP 401 w 1 HETATM 26 N N3 ADP . . . XA 35 192.431 148.127 170.669 0.5 57.54 ? N3 ADP 401 w 1 HETATM 27 C C4 ADP . . . XA 35 192.238 146.879 170.19 0.5 57.54 ? C4 ADP 401 w 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 119 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #