data_6YNX # _model_server_result.job_id jnFibcXqXecBIvK6DFRWaw _model_server_result.datetime_utc '2025-02-27 01:21:29' _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 6ynx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DB","auth_seq_id":301}' # _entry.id 6YNX # _exptl.entry_id 6YNX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 507.181 _entity.id 26 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 6YNX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YNX _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 41-meric _pdbx_struct_assembly.oligomeric_count 41 _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,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,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,KC,LC,MC _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 26 DB N N ? 26 CC 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 disulf ? disulf1 J SG CYS 125 j CYS 125 1_555 J SG CYS 155 j CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 M SG CYS 109 n CYS 109 1_555 M SG CYS 144 n CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 N SG CYS 120 o CYS 120 1_555 N SG CYS 132 o CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 CA SG CYS 125 J CYS 125 1_555 CA SG CYS 155 J CYS 155 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 FA SG CYS 109 N CYS 109 1_555 FA SG CYS 144 N CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf6 GA SG CYS 120 O CYS 120 1_555 GA SG CYS 132 O CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 C N GLY 208 d GLY 208 1_555 SA O14 PC1 . d PC1 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale2 D CG2 THR 37 f THR 37 1_555 WA OB4 CDL . f CDL 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale3 D NZ LYS 104 f LYS 104 1_555 UA OB7 CDL . f CDL 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.296 ? covale ? covale4 H NH1 ARG 144 g ARG 144 1_555 FB O12 PC1 . g PC1 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale5 U NH2 ARG 112 B ARG 112 1_555 UB OA4 CDL . B CDL 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? covale ? covale6 U NH2 ARG 172 B ARG 172 1_555 SB OB4 CDL . B CDL 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.299 ? covale ? covale7 V N GLY 208 D GLY 208 1_555 VB O14 PC1 . D PC1 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale8 X ND2 ASN 50 I ASN 50 1_555 XB OB3 CDL . I CDL 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale9 AA NH1 ARG 144 G ARG 144 1_555 FC O12 PC1 . G PC1 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale10 CA NZ LYS 98 J LYS 98 1_555 IC O2P PEE . J PEE 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.298 ? metalc ? metalc1 H OD1 ASP 151 g ASP 151 1_555 EB MG MG . g MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc2 H OD2 ASP 151 g ASP 151 1_555 EB MG MG . g MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc3 H O PHE 152 g PHE 152 1_555 EB MG MG . g MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc4 DB O1G ATP . g ATP 301 1_555 EB MG MG . g MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc5 DB O1B ATP . g ATP 301 1_555 EB MG MG . g MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc6 AA OD1 ASP 151 G ASP 151 1_555 DC MG MG . G MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc7 AA OD2 ASP 151 G ASP 151 1_555 DC MG MG . G MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc8 AA O PHE 152 G PHE 152 1_555 DC MG MG . G MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? metalc ? metalc9 CC O1G ATP . G ATP 301 1_555 DC MG MG . G MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc10 CC O1B ATP . G ATP 301 1_555 DC MG MG . G MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6YNX _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 PA 22 CDL a 1 501 5 CDL CDL . QA 22 CDL b 1 401 6 CDL CDL . RA 22 CDL b 1 402 9 CDL CDL . SA 23 PC1 d 1 301 10 PC1 PC1 . TA 24 PO4 f 1 301 900 PO4 PO4 . UA 22 CDL f 1 302 8 CDL CDL . VA 22 CDL f 1 303 11 CDL CDL . WA 22 CDL f 1 304 21 CDL CDL . XA 23 PC1 i 1 301 15 PC1 PC1 . YA 22 CDL i 1 302 18 CDL CDL . ZA 25 UQ8 i 1 303 19 UQ8 UQ8 . AB 22 CDL k 1 201 1 CDL CDL . BB 22 CDL k 1 202 17 CDL CDL . CB 22 CDL k 1 203 20 CDL CDL . DB 26 ATP g 1 301 900 ATP ATP . EB 27 MG g 1 302 901 MG MG . FB 23 PC1 g 1 303 16 PC1 PC1 . GB 22 CDL j 1 301 2 CDL CDL . HB 22 CDL j 1 302 3 CDL CDL . IB 22 CDL l 1 301 7 CDL CDL . JB 28 PEE l 1 302 12 PEE PEE . KB 28 PEE l 1 303 13 PEE PEE . LB 22 CDL l 1 304 20 CDL CDL . MB 22 CDL p 1 201 14 CDL CDL . NB 22 CDL r 1 201 4 CDL CDL . OB 29 NAD e 1 900 900 NAD NAD . PB 22 CDL A 1 501 5 CDL CDL . QB 22 CDL B 1 401 21 CDL CDL . RB 22 CDL B 1 402 6 CDL CDL . SB 22 CDL B 1 403 8 CDL CDL . TB 22 CDL B 1 404 9 CDL CDL . UB 22 CDL B 1 405 11 CDL CDL . VB 23 PC1 D 1 301 10 PC1 PC1 . WB 24 PO4 F 1 900 900 PO4 PO4 . XB 22 CDL I 1 301 4 CDL CDL . YB 22 CDL I 1 302 18 CDL CDL . ZB 25 UQ8 I 1 303 19 UQ8 UQ8 . AC 22 CDL K 1 201 1 CDL CDL . BC 22 CDL K 1 202 17 CDL CDL . CC 26 ATP G 1 301 900 ATP ATP . DC 27 MG G 1 302 901 MG MG . EC 23 PC1 G 1 303 15 PC1 PC1 . FC 23 PC1 G 1 304 16 PC1 PC1 . GC 22 CDL J 1 301 2 CDL CDL . HC 22 CDL J 1 302 3 CDL CDL . IC 28 PEE J 1 303 12 PEE PEE . JC 28 PEE J 1 304 13 PEE PEE . KC 22 CDL L 1 301 7 CDL CDL . LC 22 CDL P 1 201 14 CDL CDL . MC 29 NAD E 1 900 900 NAD NAD . # 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 PG ATP . . . DB 26 177.647 229.174 256.345 1 53.66 ? PG ATP 301 g 1 HETATM 2 O O1G ATP . . . DB 26 176.591 228.488 255.519 1 53.66 ? O1G ATP 301 g 1 HETATM 3 O O2G ATP . . . DB 26 178.45 228.141 257.097 1 53.66 ? O2G ATP 301 g 1 HETATM 4 O O3G ATP . . . DB 26 177.004 230.13 257.319 1 53.66 ? O3G ATP 301 g 1 HETATM 5 P PB ATP . . . DB 26 179.298 229.353 253.988 1 53.66 ? PB ATP 301 g 1 HETATM 6 O O1B ATP . . . DB 26 178.266 228.495 253.317 1 53.66 ? O1B ATP 301 g 1 HETATM 7 O O2B ATP . . . DB 26 180.479 228.518 254.366 1 53.66 ? O2B ATP 301 g 1 HETATM 8 O O3B ATP . . . DB 26 178.641 230.026 255.333 1 53.66 ? O3B ATP 301 g 1 HETATM 9 P PA ATP . . . DB 26 178.784 231.678 252.293 1 53.66 ? PA ATP 301 g 1 HETATM 10 O O1A ATP . . . DB 26 178.042 232.402 253.361 1 53.66 ? O1A ATP 301 g 1 HETATM 11 O O2A ATP . . . DB 26 177.81 231.029 251.36 1 53.66 ? O2A ATP 301 g 1 HETATM 12 O O3A ATP . . . DB 26 179.78 230.536 252.948 1 53.66 ? O3A ATP 301 g 1 HETATM 13 O O5' ATP . . . DB 26 179.705 232.713 251.466 1 53.66 ? O5' ATP 301 g 1 HETATM 14 C C5' ATP . . . DB 26 180.145 232.255 250.211 1 53.66 ? C5' ATP 301 g 1 HETATM 15 C C4' ATP . . . DB 26 181.565 232.837 249.871 1 53.66 ? C4' ATP 301 g 1 HETATM 16 O O4' ATP . . . DB 26 181.405 234.34 249.554 1 53.66 ? O4' ATP 301 g 1 HETATM 17 C C3' ATP . . . DB 26 182.377 232.766 250.861 1 53.66 ? C3' ATP 301 g 1 HETATM 18 O O3' ATP . . . DB 26 183.232 231.585 250.726 1 53.66 ? O3' ATP 301 g 1 HETATM 19 C C2' ATP . . . DB 26 183.305 234.135 250.796 1 53.66 ? C2' ATP 301 g 1 HETATM 20 O O2' ATP . . . DB 26 184.49 233.883 249.971 1 53.66 ? O2' ATP 301 g 1 HETATM 21 C C1' ATP . . . DB 26 182.596 235.049 250.267 1 53.66 ? C1' ATP 301 g 1 HETATM 22 N N9 ATP . . . DB 26 182.071 235.972 251.301 1 53.66 ? N9 ATP 301 g 1 HETATM 23 C C8 ATP . . . DB 26 181.067 235.487 252.025 1 53.66 ? C8 ATP 301 g 1 HETATM 24 N N7 ATP . . . DB 26 180.707 236.432 252.903 1 53.66 ? N7 ATP 301 g 1 HETATM 25 C C5 ATP . . . DB 26 181.498 237.496 252.703 1 53.66 ? C5 ATP 301 g 1 HETATM 26 C C6 ATP . . . DB 26 181.563 238.719 253.312 1 53.66 ? C6 ATP 301 g 1 HETATM 27 N N6 ATP . . . DB 26 180.795 239.297 254.394 1 53.66 ? N6 ATP 301 g 1 HETATM 28 N N1 ATP . . . DB 26 182.454 239.61 252.92 1 53.66 ? N1 ATP 301 g 1 HETATM 29 C C2 ATP . . . DB 26 183.303 239.313 251.915 1 53.66 ? C2 ATP 301 g 1 HETATM 30 N N3 ATP . . . DB 26 183.246 238.117 251.31 1 53.66 ? N3 ATP 301 g 1 HETATM 31 C C4 ATP . . . DB 26 182.341 237.214 251.712 1 53.66 ? C4 ATP 301 g 1 HETATM 32 H "H5'1" ATP . . . DB 26 180.202 231.289 250.231 1 53.66 ? "H5'1" ATP 301 g 1 HETATM 33 H "H5'2" ATP . . . DB 26 179.523 232.535 249.525 1 53.66 ? "H5'2" ATP 301 g 1 HETATM 34 H H4' ATP . . . DB 26 181.941 232.377 249.108 1 53.66 ? H4' ATP 301 g 1 HETATM 35 H H3' ATP . . . DB 26 181.905 232.739 251.702 1 53.66 ? H3' ATP 301 g 1 HETATM 36 H H2' ATP . . . DB 26 183.566 234.396 251.689 1 53.66 ? H2' ATP 301 g 1 HETATM 37 H HO2' ATP . . . DB 26 185.12 233.601 250.466 1 53.66 ? HO2' ATP 301 g 1 HETATM 38 H H1' ATP . . . DB 26 183.121 235.536 249.616 1 53.66 ? H1' ATP 301 g 1 HETATM 39 H H8 ATP . . . DB 26 180.691 234.646 251.938 1 53.66 ? H8 ATP 301 g 1 HETATM 40 H HN61 ATP . . . DB 26 180.197 239.885 254.225 1 53.66 ? HN61 ATP 301 g 1 HETATM 41 H HN62 ATP . . . DB 26 180.94 239.05 255.201 1 53.66 ? HN62 ATP 301 g 1 HETATM 42 H H2 ATP . . . DB 26 183.926 239.94 251.637 1 53.66 ? H2 ATP 301 g 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 457 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 42 #