data_5GJR # _model_server_result.job_id dh7ZvVnc-bSxpnTEHY6Qpw _model_server_result.datetime_utc '2024-11-23 22:43:57' _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 5gjr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"UB","auth_seq_id":501}' # _entry.id 5GJR # _exptl.entry_id 5GJR _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 33 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 12 _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 5GJR _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GJR _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 64-meric _pdbx_struct_assembly.oligomeric_count 64 _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 _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 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 ? 33 MB N N ? 33 NB N N ? 33 OB N N ? 33 PB N N ? 33 QB N N ? 33 RB N N ? 33 SB N N ? 33 TB N N ? 33 UB N N ? 33 VB N N ? 33 WB N N ? 33 XB 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 covale ? covale1 N O ILE 91 U ILE 91 1_555 N SG CYS 116 U CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? covale ? covale2 HB O ILE 91 8 ILE 91 1_555 HB SG CYS 116 8 CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? # _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 5GJR _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 MB 33 ADP I 1 501 501 ADP ADP . NB 33 ADP H 1 501 501 ADP ADP . OB 33 ADP L 1 401 401 ADP ADP . PB 33 ADP M 1 501 501 ADP ADP . QB 33 ADP J 1 501 501 ADP ADP . RB 33 ADP K 1 501 501 ADP ADP . SB 33 ADP v 1 501 501 ADP ADP . TB 33 ADP w 1 501 501 ADP ADP . UB 33 ADP x 1 501 501 ADP ADP . VB 33 ADP y 1 501 501 ADP ADP . WB 33 ADP z 1 401 401 ADP ADP . XB 33 ADP 0 1 501 501 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 . . . UB 33 180.913 314.658 267.744 1 20 ? PB ADP 501 x 1 HETATM 2 O O1B ADP . . . UB 33 180.364 314.509 266.349 1 20 ? O1B ADP 501 x 1 HETATM 3 O O2B ADP . . . UB 33 182.075 315.614 267.847 1 20 ? O2B ADP 501 x 1 HETATM 4 O O3B ADP . . . UB 33 181.074 313.367 268.508 1 20 ? O3B ADP 501 x 1 HETATM 5 P PA ADP . . . UB 33 178.813 316.401 267.687 1 20 ? PA ADP 501 x 1 HETATM 6 O O1A ADP . . . UB 33 179.66 316.953 266.569 1 20 ? O1A ADP 501 x 1 HETATM 7 O O2A ADP . . . UB 33 177.512 315.703 267.397 1 20 ? O2A ADP 501 x 1 HETATM 8 O O3A ADP . . . UB 33 179.73 315.398 268.527 1 20 ? O3A ADP 501 x 1 HETATM 9 O O5' ADP . . . UB 33 178.521 317.58 268.73 1 20 ? O5' ADP 501 x 1 HETATM 10 C C5' ADP . . . UB 33 177.249 318.213 268.722 1 20 ? C5' ADP 501 x 1 HETATM 11 C C4' ADP . . . UB 33 177.425 319.629 269.241 1 20 ? C4' ADP 501 x 1 HETATM 12 O O4' ADP . . . UB 33 178.68 320.128 268.788 1 20 ? O4' ADP 501 x 1 HETATM 13 C C3' ADP . . . UB 33 176.344 320.557 268.718 1 20 ? C3' ADP 501 x 1 HETATM 14 O O3' ADP . . . UB 33 175.541 321.025 269.801 1 20 ? O3' ADP 501 x 1 HETATM 15 C C2' ADP . . . UB 33 177.064 321.725 268.086 1 20 ? C2' ADP 501 x 1 HETATM 16 O O2' ADP . . . UB 33 176.691 322.939 268.739 1 20 ? O2' ADP 501 x 1 HETATM 17 C C1' ADP . . . UB 33 178.541 321.454 268.286 1 20 ? C1' ADP 501 x 1 HETATM 18 N N9 ADP . . . UB 33 179.226 321.549 266.983 1 20 ? N9 ADP 501 x 1 HETATM 19 C C8 ADP . . . UB 33 179.983 320.597 266.415 1 20 ? C8 ADP 501 x 1 HETATM 20 N N7 ADP . . . UB 33 180.463 321.012 265.217 1 20 ? N7 ADP 501 x 1 HETATM 21 C C5 ADP . . . UB 33 180.003 322.257 265.013 1 20 ? C5 ADP 501 x 1 HETATM 22 C C6 ADP . . . UB 33 180.126 323.277 263.954 1 20 ? C6 ADP 501 x 1 HETATM 23 N N6 ADP . . . UB 33 180.859 323.044 262.842 1 20 ? N6 ADP 501 x 1 HETATM 24 N N1 ADP . . . UB 33 179.484 324.447 264.133 1 20 ? N1 ADP 501 x 1 HETATM 25 C C2 ADP . . . UB 33 178.753 324.692 265.232 1 20 ? C2 ADP 501 x 1 HETATM 26 N N3 ADP . . . UB 33 178.599 323.814 266.231 1 20 ? N3 ADP 501 x 1 HETATM 27 C C4 ADP . . . UB 33 179.189 322.604 266.178 1 20 ? C4 ADP 501 x 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 190 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #