data_2GXA # _model_server_result.job_id vazglyRfP8VRuJCv0ZHpDQ _model_server_result.datetime_utc '2025-02-05 12:02:15' _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 2gxa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":5}' # _entry.id 2GXA # _exptl.entry_id 2GXA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 11 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 92.6 _cell.angle_beta 111.46 _cell.angle_gamma 106.01 _cell.entry_id 2GXA _cell.length_a 100.51 _cell.length_b 100.881 _cell.length_c 125.023 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GXA _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 ? heptameric 7 author_defined_assembly 1 ? heptameric 7 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,MA,NA,OA,PA 1 1 B,I,J,K,L,M,N,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,QA,RA,SA 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 ? 5 Q N N ? 5 T N N ? 5 V N N ? 5 X N N ? 5 Z N N ? 5 AA N N ? 5 CA N N ? 5 FA N N ? 5 IA N N ? 5 KA N N ? 5 LA 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 Q O1B ADP . A ADP 1 1_555 O MG MG . A MG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc2 Q O3B ADP . A ADP 1 1_555 O MG MG . A MG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc3 O MG MG . A MG 21 1_555 C OG SER 137 A SER 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.954 ? metalc ? metalc4 O MG MG . A MG 21 1_555 MA O HOH . A HOH 578 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc5 O MG MG . A MG 21 1_555 MA O HOH . A HOH 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc6 O MG MG . A MG 21 1_555 NA O HOH . B HOH 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc7 O MG MG . A MG 21 1_555 D NH2 ARG 235 B ARG 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.099 ? metalc ? metalc8 T O3B ADP . B ADP 2 1_555 R MG MG . B MG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc9 T O1B ADP . B ADP 2 1_555 R MG MG . B MG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc10 NA O HOH . B HOH 4 1_555 R MG MG . B MG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc11 NA O HOH . B HOH 6 1_555 R MG MG . B MG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc12 R MG MG . B MG 22 1_555 D OG SER 137 B SER 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc13 R MG MG . B MG 22 1_555 D OD2 ASP 176 B ASP 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.912 ? metalc ? metalc14 R MG MG . B MG 22 1_555 OA O HOH . C HOH 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc15 R MG MG . B MG 22 1_555 E NH2 ARG 235 C ARG 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.074 ? metalc ? metalc16 V O1B ADP . C ADP 3 1_555 U MG MG . C MG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc17 OA O HOH . C HOH 7 1_555 U MG MG . C MG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc18 OA O HOH . C HOH 8 1_555 U MG MG . C MG 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.945 ? metalc ? metalc19 U MG MG . C MG 23 1_555 E OG SER 137 C SER 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc20 U MG MG . C MG 23 1_555 E OD2 ASP 176 C ASP 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc21 U MG MG . C MG 23 1_555 PA O HOH . D HOH 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.782 ? metalc ? metalc22 X O3B ADP . D ADP 4 1_555 W MG MG . D MG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.053 ? metalc ? metalc23 X O1B ADP . D ADP 4 1_555 W MG MG . D MG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc24 W MG MG . D MG 24 1_555 F OG SER 137 D SER 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc25 Z O1B ADP . E ADP 5 1_555 Y MG MG . E MG 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.007 ? metalc ? metalc26 Z O3B ADP . E ADP 5 1_555 Y MG MG . E MG 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc27 Y MG MG . E MG 25 1_555 G OG SER 137 E SER 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc28 CA O1B ADP . G ADP 7 1_555 BA MG MG . G MG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc29 CA O3B ADP . G ADP 7 1_555 BA MG MG . G MG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc30 QA O HOH . G HOH 10 1_555 BA MG MG . G MG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc31 QA O HOH . G HOH 11 1_555 BA MG MG . G MG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc32 QA O HOH . G HOH 12 1_555 BA MG MG . G MG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc33 BA MG MG . G MG 27 1_555 I OG SER 137 G SER 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc34 FA O1B ADP . H ADP 8 1_555 DA MG MG . H MG 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc35 RA O HOH . H HOH 13 1_555 DA MG MG . H MG 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.692 ? metalc ? metalc36 RA O HOH . H HOH 14 1_555 DA MG MG . H MG 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? metalc ? metalc37 DA MG MG . H MG 28 1_555 J OG SER 137 H SER 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc38 DA MG MG . H MG 28 1_555 J OD2 ASP 176 H ASP 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? metalc ? metalc39 DA MG MG . H MG 28 1_555 SA O HOH . I HOH 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc40 GA MG MG . I MG 29 1_555 K OG SER 137 I SER 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc41 GA MG MG . I MG 29 1_555 K OD2 ASP 176 I ASP 479 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? metalc ? metalc42 GA MG MG . I MG 29 1_555 IA O1B ADP . J ADP 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? metalc ? metalc43 HA MG MG . J MG 30 1_555 L OG SER 137 J SER 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc44 HA MG MG . J MG 30 1_555 KA O1B ADP . K ADP 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc45 HA MG MG . J MG 30 1_555 KA O3B ADP . K ADP 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? metalc ? metalc46 JA MG MG . K MG 31 1_555 M OG SER 137 K SER 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc47 JA MG MG . K MG 31 1_555 LA O3B ADP . L ADP 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? metalc ? metalc48 JA MG MG . K MG 31 1_555 LA O2A ADP . L ADP 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc49 JA MG MG . K MG 31 1_555 LA O1A ADP . L ADP 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? # _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 2GXA _atom_sites.fract_transf_matrix[1][1] 0.009949 _atom_sites.fract_transf_matrix[1][2] 0.002856 _atom_sites.fract_transf_matrix[1][3] 0.004437 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010313 _atom_sites.fract_transf_matrix[2][3] 0.001709 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.008711 _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 O 3 MG A 1 21 1 MG MG2 . P 4 CL A 1 41 1 CL CL1 . Q 5 ADP A 1 1 1 ADP ADP . R 3 MG B 1 22 2 MG MG2 . S 4 CL B 1 42 2 CL CL1 . T 5 ADP B 1 2 2 ADP ADP . U 3 MG C 1 23 3 MG MG2 . V 5 ADP C 1 3 3 ADP ADP . W 3 MG D 1 24 4 MG MG2 . X 5 ADP D 1 4 4 ADP ADP . Y 3 MG E 1 25 5 MG MG2 . Z 5 ADP E 1 5 5 ADP ADP . AA 5 ADP F 1 6 6 ADP ADP . BA 3 MG G 1 27 7 MG MG2 . CA 5 ADP G 1 7 7 ADP ADP . DA 3 MG H 1 28 8 MG MG2 . EA 4 CL H 1 48 8 CL CL1 . FA 5 ADP H 1 8 8 ADP ADP . GA 3 MG I 1 29 9 MG MG2 . HA 3 MG J 1 30 10 MG MG2 . IA 5 ADP J 1 9 9 ADP ADP . JA 3 MG K 1 31 11 MG MG2 . KA 5 ADP K 1 10 10 ADP ADP . LA 5 ADP L 1 11 11 ADP ADP . MA 6 HOH A 1 578 1 HOH HOH . MA 6 HOH A 2 579 2 HOH HOH . NA 6 HOH B 1 3 3 HOH HOH . NA 6 HOH B 2 4 4 HOH HOH . NA 6 HOH B 3 6 6 HOH HOH . OA 6 HOH C 1 5 5 HOH HOH . OA 6 HOH C 2 7 7 HOH HOH . OA 6 HOH C 3 8 8 HOH HOH . PA 6 HOH D 1 9 9 HOH HOH . QA 6 HOH G 1 10 10 HOH HOH . QA 6 HOH G 2 11 11 HOH HOH . QA 6 HOH G 3 12 12 HOH HOH . RA 6 HOH H 1 13 13 HOH HOH . RA 6 HOH H 2 14 14 HOH HOH . SA 6 HOH I 1 15 15 HOH HOH . # 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 . . . Z 5 -7.572 61.573 -15.228 1 77.6 ? PB ADP 5 E 1 HETATM 2 O O1B ADP . . . Z 5 -7.368 61.017 -13.887 1 77.6 ? O1B ADP 5 E 1 HETATM 3 O O2B ADP . . . Z 5 -9.115 61.438 -15.636 1 77.6 ? O2B ADP 5 E 1 HETATM 4 O O3B ADP . . . Z 5 -6.68 60.779 -16.31 1 77.6 ? O3B ADP 5 E 1 HETATM 5 P PA ADP . . . Z 5 -5.623 63.344 -14.846 1 77.6 ? PA ADP 5 E 1 HETATM 6 O O1A ADP . . . Z 5 -5.475 63.032 -13.409 1 77.6 ? O1A ADP 5 E 1 HETATM 7 O O2A ADP . . . Z 5 -4.664 62.389 -15.719 1 77.6 ? O2A ADP 5 E 1 HETATM 8 O O3A ADP . . . Z 5 -7.173 63.145 -15.261 1 77.6 ? O3A ADP 5 E 1 HETATM 9 O O5' ADP . . . Z 5 -5.267 64.908 -15.052 1 195.34 ? O5' ADP 5 E 1 HETATM 10 C C5' ADP . . . Z 5 -3.869 65.108 -14.818 1 195.34 ? C5' ADP 5 E 1 HETATM 11 C C4' ADP . . . Z 5 -3.542 66.582 -15.071 1 195.34 ? C4' ADP 5 E 1 HETATM 12 O O4' ADP . . . Z 5 -4.247 67.432 -14.115 1 195.34 ? O4' ADP 5 E 1 HETATM 13 C C3' ADP . . . Z 5 -2.034 66.867 -14.934 1 195.34 ? C3' ADP 5 E 1 HETATM 14 O O3' ADP . . . Z 5 -1.502 67.322 -16.186 1 195.34 ? O3' ADP 5 E 1 HETATM 15 C C2' ADP . . . Z 5 -1.876 67.909 -13.841 1 195.34 ? C2' ADP 5 E 1 HETATM 16 O O2' ADP . . . Z 5 -1.234 69.093 -14.331 1 195.34 ? O2' ADP 5 E 1 HETATM 17 C C1' ADP . . . Z 5 -3.286 68.197 -13.319 1 195.34 ? C1' ADP 5 E 1 HETATM 18 N N9 ADP . . . Z 5 -3.307 67.798 -11.909 0 105.05 ? N9 ADP 5 E 1 HETATM 19 C C8 ADP . . . Z 5 -3.835 66.653 -11.388 0 105.05 ? C8 ADP 5 E 1 HETATM 20 N N7 ADP . . . Z 5 -3.675 66.629 -10.095 0 105.05 ? N7 ADP 5 E 1 HETATM 21 C C5 ADP . . . Z 5 -3.033 67.758 -9.711 0 105.05 ? C5 ADP 5 E 1 HETATM 22 C C6 ADP . . . Z 5 -2.592 68.282 -8.468 0 105.05 ? C6 ADP 5 E 1 HETATM 23 N N6 ADP . . . Z 5 -2.801 67.571 -7.297 0 105.05 ? N6 ADP 5 E 1 HETATM 24 N N1 ADP . . . Z 5 -1.962 69.481 -8.456 0 105.05 ? N1 ADP 5 E 1 HETATM 25 C C2 ADP . . . Z 5 -1.754 70.182 -9.586 0 105.05 ? C2 ADP 5 E 1 HETATM 26 N N3 ADP . . . Z 5 -2.154 69.718 -10.765 0 105.05 ? N3 ADP 5 E 1 HETATM 27 C C4 ADP . . . Z 5 -2.799 68.528 -10.867 0 105.05 ? C4 ADP 5 E 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #