data_6WM4 # _model_server_result.job_id v_do4CCHB99hgqxMuiIdgw _model_server_result.datetime_utc '2024-12-02 01:23:04' _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 6wm4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"LA","auth_seq_id":701}' # _entry.id 6WM4 # _exptl.entry_id 6WM4 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 19 _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 6WM4 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6WM4 _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 35-meric _pdbx_struct_assembly.oligomeric_count 35 _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 _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 19 _struct_asym.id LA _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 V SG CYS 371 U CYS 371 1_555 V SG CYS 418 U CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 488 R ASN 488 1_555 JA C1 NAG . R NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 V ND2 ASN 261 U ASN 261 1_555 OA C1 NAG . U NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 V ND2 ASN 273 U ASN 273 1_555 RA C1 NAG . U NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 V ND2 ASN 296 U ASN 296 1_555 NA C1 NAG . U NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 V ND2 ASN 303 U ASN 303 1_555 PA C1 NAG . U NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale6 V ND2 ASN 350 U ASN 350 1_555 MA C1 NAG . U NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 V ND2 ASN 357 U ASN 357 1_555 QA C1 NAG . U NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 6WM4 _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 JA 18 NAG R 1 901 833 NAG NAG . KA 18 NAG R 1 902 81 NAG NAG . LA 19 ADP A 1 701 1 ADP ADP . MA 18 NAG U 1 501 459 NAG NAG . NA 18 NAG U 1 502 460 NAG NAG . OA 18 NAG U 1 503 461 NAG NAG . PA 18 NAG U 1 504 462 NAG NAG . QA 18 NAG U 1 505 463 NAG NAG . RA 18 NAG U 1 506 464 NAG NAG . # 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 . . . LA 19 143.817 154.881 189.75 1 27.41 ? PB ADP 701 A 1 HETATM 2 O O1B ADP . . . LA 19 144.097 155.801 188.6 1 27.41 ? O1B ADP 701 A 1 HETATM 3 O O2B ADP . . . LA 19 142.458 154.234 189.718 1 27.41 ? O2B ADP 701 A 1 HETATM 4 O O3B ADP . . . LA 19 144.949 153.95 190.081 1 27.41 ? O3B ADP 701 A 1 HETATM 5 P PA ADP . . . LA 19 142.544 156.925 191.105 1 27.41 ? PA ADP 701 A 1 HETATM 6 O O1A ADP . . . LA 19 142.56 157.76 189.861 1 27.41 ? O1A ADP 701 A 1 HETATM 7 O O2A ADP . . . LA 19 141.306 156.151 191.459 1 27.41 ? O2A ADP 701 A 1 HETATM 8 O O3A ADP . . . LA 19 143.762 155.897 190.988 1 27.41 ? O3A ADP 701 A 1 HETATM 9 O O5' ADP . . . LA 19 142.935 157.845 192.354 1 27.41 ? O5' ADP 701 A 1 HETATM 10 C C5' ADP . . . LA 19 144.027 158.741 192.231 1 27.41 ? C5' ADP 701 A 1 HETATM 11 C C4' ADP . . . LA 19 144.338 159.413 193.56 1 27.41 ? C4' ADP 701 A 1 HETATM 12 O O4' ADP . . . LA 19 145.226 160.5 193.32 1 27.41 ? O4' ADP 701 A 1 HETATM 13 C C3' ADP . . . LA 19 143.101 159.991 194.208 1 27.41 ? C3' ADP 701 A 1 HETATM 14 O O3' ADP . . . LA 19 142.772 159.254 195.38 1 27.41 ? O3' ADP 701 A 1 HETATM 15 C C2' ADP . . . LA 19 143.486 161.379 194.632 1 27.41 ? C2' ADP 701 A 1 HETATM 16 O O2' ADP . . . LA 19 143.824 161.347 196.015 1 27.41 ? O2' ADP 701 A 1 HETATM 17 C C1' ADP . . . LA 19 144.714 161.722 193.833 1 27.41 ? C1' ADP 701 A 1 HETATM 18 N N9 ADP . . . LA 19 144.24 162.541 192.698 1 27.41 ? N9 ADP 701 A 1 HETATM 19 C C8 ADP . . . LA 19 144.026 162.095 191.453 1 27.41 ? C8 ADP 701 A 1 HETATM 20 N N7 ADP . . . LA 19 143.587 163.084 190.642 1 27.41 ? N7 ADP 701 A 1 HETATM 21 C C5 ADP . . . LA 19 143.507 164.193 191.383 1 27.41 ? C5 ADP 701 A 1 HETATM 22 C C6 ADP . . . LA 19 143.107 165.587 191.146 1 27.41 ? C6 ADP 701 A 1 HETATM 23 N N6 ADP . . . LA 19 142.699 165.996 189.923 1 27.41 ? N6 ADP 701 A 1 HETATM 24 N N1 ADP . . . LA 19 143.166 166.433 192.189 1 27.41 ? N1 ADP 701 A 1 HETATM 25 C C2 ADP . . . LA 19 143.569 166.035 193.405 1 27.41 ? C2 ADP 701 A 1 HETATM 26 N N3 ADP . . . LA 19 143.942 164.784 193.69 1 27.41 ? N3 ADP 701 A 1 HETATM 27 C C4 ADP . . . LA 19 143.934 163.833 192.736 1 27.41 ? C4 ADP 701 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 123 _model_server_stats.query_time_ms 430 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #