data_2BUF # _model_server_result.job_id FXflOJo54oR5N-E1p-yoHg _model_server_result.datetime_utc '2025-01-02 22:55:58' _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 2buf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":1299}' # _entry.id 2BUF # _exptl.entry_id 2BUF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 10 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 91.49 _cell.angle_beta 92.03 _cell.angle_gamma 107.56 _cell.entry_id 2BUF _cell.length_a 71.86 _cell.length_b 98.78 _cell.length_c 162.9 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BUF _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 PQS hexameric 6 author_and_software_defined_assembly 1 PQS hexameric 6 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,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA 1 1 G,H,I,J,K,L,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA 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 ? 3 N N N ? 3 R N N ? 3 U N N ? 3 Y N N ? 3 BA N N ? 3 DA N N ? 3 HA N N ? 3 LA N N ? 3 OA N N ? 3 QA 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 N O1B ADP . B ADP 1300 1_555 O MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc2 N O2A ADP . B ADP 1300 1_555 O MG MG . B MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? metalc ? metalc3 R O2A ADP . C ADP 1300 1_555 S MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc4 R O2B ADP . C ADP 1300 1_555 S MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.049 ? metalc ? metalc5 R O3A ADP . C ADP 1300 1_555 S MG MG . C MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc6 U O1B ADP . D ADP 1300 1_555 V MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.13 ? metalc ? metalc7 U O3B ADP . D ADP 1300 1_555 V MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc8 U O2A ADP . D ADP 1300 1_555 V MG MG . D MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.079 ? metalc ? metalc9 Y O3B ADP . E ADP 1299 1_555 Z MG MG . E MG 1300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc10 Y O2A ADP . E ADP 1299 1_555 Z MG MG . E MG 1300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.77 ? metalc ? metalc11 DA O2A ADP . G ADP 1299 1_555 EA MG MG . G MG 1300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.096 ? metalc ? metalc12 DA O3A ADP . G ADP 1299 1_555 EA MG MG . G MG 1300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc13 DA O1B ADP . G ADP 1299 1_555 EA MG MG . G MG 1300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc14 H ND2 ASN 36 H ASN 37 1_555 IA MG MG . H MG 1298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc15 HA O3B ADP . H ADP 1297 1_555 IA MG MG . H MG 1298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc16 HA O3A ADP . H ADP 1297 1_555 IA MG MG . H MG 1298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc17 LA O1B ADP . I ADP 1298 1_555 MA MG MG . I MG 1299 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc18 LA O2A ADP . I ADP 1298 1_555 MA MG MG . I MG 1299 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.003 ? metalc ? metalc19 QA O2A ADP . L ADP 1300 1_555 RA MG MG . L MG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? # _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 2BUF _atom_sites.fract_transf_matrix[1][1] 0.013916 _atom_sites.fract_transf_matrix[1][2] 0.004404 _atom_sites.fract_transf_matrix[1][3] 0.000663 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010618 _atom_sites.fract_transf_matrix[2][3] 0.000409 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006147 _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 M 2 NLG A 1 1302 1302 NLG NLG . N 3 ADP B 1 1300 1300 ADP ADP . O 4 MG B 1 1301 1301 MG MG . P 2 NLG B 1 1302 1302 NLG NLG . Q 5 CL B 1 1303 1303 CL CL . R 3 ADP C 1 1300 1300 ADP ADP . S 4 MG C 1 1301 1301 MG MG . T 5 CL C 1 1302 1302 CL CL . U 3 ADP D 1 1300 1300 ADP ADP . V 4 MG D 1 1301 1301 MG MG . W 2 NLG D 1 1302 1302 NLG NLG . X 5 CL D 1 1303 1303 CL CL . Y 3 ADP E 1 1299 1299 ADP ADP . Z 4 MG E 1 1300 1300 MG MG . AA 2 NLG E 1 1301 1301 NLG NLG . BA 3 ADP F 1 1299 1299 ADP ADP . CA 2 NLG F 1 1300 1300 NLG NLG . DA 3 ADP G 1 1299 1299 ADP ADP . EA 4 MG G 1 1300 1300 MG MG . FA 2 NLG G 1 1301 1301 NLG NLG . GA 5 CL G 1 1302 1302 CL CL . HA 3 ADP H 1 1297 1297 ADP ADP . IA 4 MG H 1 1298 1298 MG MG . JA 2 NLG H 1 1299 1299 NLG NLG . KA 5 CL H 1 1300 1300 CL CL . LA 3 ADP I 1 1298 1298 ADP ADP . MA 4 MG I 1 1299 1299 MG MG . NA 2 NLG I 1 1300 1300 NLG NLG . OA 3 ADP J 1 1298 1298 ADP ADP . PA 2 NLG K 1 1298 1298 NLG NLG . QA 3 ADP L 1 1300 1300 ADP ADP . RA 4 MG L 1 1301 1301 MG MG . SA 2 NLG L 1 1302 1302 NLG NLG . TA 5 CL L 1 1303 1303 CL CL . # 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 . . . DA 3 3.576 -22.442 -54.73 1 120.78 ? PB ADP 1299 G 1 HETATM 2 O O1B ADP . . . DA 3 3.082 -22.475 -56.18 1 120.59 ? O1B ADP 1299 G 1 HETATM 3 O O2B ADP . . . DA 3 4.485 -21.324 -54.395 1 120.77 ? O2B ADP 1299 G 1 HETATM 4 O O3B ADP . . . DA 3 2.373 -22.543 -53.735 1 120.92 ? O3B ADP 1299 G 1 HETATM 5 P PA ADP . . . DA 3 5.677 -24.519 -54.984 1 114.53 ? PA ADP 1299 G 1 HETATM 6 O O1A ADP . . . DA 3 5.84 -25.79 -54.221 1 113.25 ? O1A ADP 1299 G 1 HETATM 7 O O2A ADP . . . DA 3 5.643 -24.741 -56.421 1 115.08 ? O2A ADP 1299 G 1 HETATM 8 O O3A ADP . . . DA 3 4.343 -23.79 -54.424 1 117.44 ? O3A ADP 1299 G 1 HETATM 9 O O5' ADP . . . DA 3 6.888 -23.508 -54.642 1 110.36 ? O5' ADP 1299 G 1 HETATM 10 C C5' ADP . . . DA 3 7.134 -23.053 -53.277 1 103.29 ? C5' ADP 1299 G 1 HETATM 11 C C4' ADP . . . DA 3 8.241 -23.77 -52.527 1 98.47 ? C4' ADP 1299 G 1 HETATM 12 O O4' ADP . . . DA 3 9.587 -23.561 -53.089 1 95.28 ? O4' ADP 1299 G 1 HETATM 13 C C3' ADP . . . DA 3 8.465 -23.307 -51.063 1 95.7 ? C3' ADP 1299 G 1 HETATM 14 O O3' ADP . . . DA 3 7.3 -23.804 -50.313 1 94.98 ? O3' ADP 1299 G 1 HETATM 15 C C2' ADP . . . DA 3 9.811 -24.018 -50.771 1 93.73 ? C2' ADP 1299 G 1 HETATM 16 O O2' ADP . . . DA 3 9.531 -25.334 -50.202 1 92.9 ? O2' ADP 1299 G 1 HETATM 17 C C1' ADP . . . DA 3 10.509 -24.135 -52.144 1 91.69 ? C1' ADP 1299 G 1 HETATM 18 N N9 ADP . . . DA 3 11.762 -23.365 -52.139 1 87.66 ? N9 ADP 1299 G 1 HETATM 19 C C8 ADP . . . DA 3 12.914 -23.818 -52.751 1 86.34 ? C8 ADP 1299 G 1 HETATM 20 N N7 ADP . . . DA 3 13.956 -23.077 -52.71 1 85.34 ? N7 ADP 1299 G 1 HETATM 21 C C5 ADP . . . DA 3 13.493 -22.018 -52.036 1 84.67 ? C5 ADP 1299 G 1 HETATM 22 C C6 ADP . . . DA 3 14.16 -20.85 -51.664 1 84.49 ? C6 ADP 1299 G 1 HETATM 23 N N6 ADP . . . DA 3 15.435 -20.464 -51.894 1 85.13 ? N6 ADP 1299 G 1 HETATM 24 N N1 ADP . . . DA 3 13.412 -19.886 -50.947 1 84.62 ? N1 ADP 1299 G 1 HETATM 25 C C2 ADP . . . DA 3 12.068 -20.14 -50.635 1 83.85 ? C2 ADP 1299 G 1 HETATM 26 N N3 ADP . . . DA 3 11.349 -21.224 -50.937 1 84.15 ? N3 ADP 1299 G 1 HETATM 27 C C4 ADP . . . DA 3 12.14 -22.149 -51.675 1 85.02 ? C4 ADP 1299 G 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #