data_4Z1M # _model_server_result.job_id V9xCsMq60r8yu8s6nWTtJw _model_server_result.datetime_utc '2025-02-26 14:44:41' _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 4z1m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":601}' # _entry.id 4Z1M # _exptl.entry_id 4Z1M _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'K39A mutation plus C-ter 6His tag' _entity.formula_weight 507.181 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation K39A _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 4Z1M _cell.length_a 108.773 _cell.length_b 155.286 _cell.length_c 271.018 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Z1M _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details decameric _pdbx_struct_assembly.oligomeric_count 10 _pdbx_struct_assembly.details author_and_software_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 _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 ? 5 K N N ? 5 N N N ? 5 R 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 A OG1 THR 176 A THR 176 1_555 L MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc2 K O2G ATP . A ATP 601 1_555 L MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc3 K O2B ATP . A ATP 601 1_555 L MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc4 L MG MG . A MG 602 1_555 HA O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc5 L MG MG . A MG 602 1_555 HA O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc6 L MG MG . A MG 602 1_555 HA O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc7 B OG1 THR 176 B THR 176 1_555 O MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc8 N O2G ATP . B ATP 601 1_555 O MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc9 N O2B ATP . B ATP 601 1_555 O MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc10 O MG MG . B MG 602 1_555 IA O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc11 O MG MG . B MG 602 1_555 IA O HOH . B HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc12 O MG MG . B MG 602 1_555 IA O HOH . B HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc13 C OG1 THR 176 C THR 176 1_555 S MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc14 R O2G ATP . C ATP 601 1_555 S MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc15 R O2B ATP . C ATP 601 1_555 S MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc16 S MG MG . C MG 602 1_555 JA O HOH . C HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc17 S MG MG . C MG 602 1_555 JA O HOH . C HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc18 S MG MG . C MG 602 1_555 JA O HOH . C HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc19 D OG1 THR 167 D THR 163 1_555 W MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc20 V O2B ADP . D ADP 600 1_555 W MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc21 W MG MG . D MG 601 1_555 KA O HOH . D HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc22 W MG MG . D MG 601 1_555 KA O HOH . D HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc23 W MG MG . D MG 601 1_555 KA O HOH . D HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc24 W MG MG . D MG 601 1_555 KA O HOH . D HOH 705 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc25 F OG1 THR 167 F THR 163 1_555 CA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc26 BA O2B ADP . F ADP 501 1_555 CA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc27 CA MG MG . F MG 502 1_555 MA O HOH . F HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc28 CA MG MG . F MG 502 1_555 MA O HOH . F HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc29 CA MG MG . F MG 502 1_555 MA O HOH . F HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc30 CA MG MG . F MG 502 1_555 MA O HOH . F HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? # _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 ? # 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 PG O1G ATP doub 114 n n PG O2G ATP sing 115 n n PG O3G ATP sing 116 n n PG O3B ATP sing 117 n n O2G HOG2 ATP sing 118 n n O3G HOG3 ATP sing 119 n n PB O1B ATP doub 120 n n PB O2B ATP sing 121 n n PB O3B ATP sing 122 n n PB O3A ATP sing 123 n n O2B HOB2 ATP sing 124 n n PA O1A ATP doub 125 n n PA O2A ATP sing 126 n n PA O3A ATP sing 127 n n PA O5' ATP sing 128 n n O2A HOA2 ATP sing 129 n n O5' C5' ATP sing 130 n n C5' C4' ATP sing 131 n n C5' "H5'1" ATP sing 132 n n C5' "H5'2" ATP sing 133 n n C4' O4' ATP sing 134 n n C4' C3' ATP sing 135 n n C4' H4' ATP sing 136 n n O4' C1' ATP sing 137 n n C3' O3' ATP sing 138 n n C3' C2' ATP sing 139 n n C3' H3' ATP sing 140 n n O3' HO3' ATP sing 141 n n C2' O2' ATP sing 142 n n C2' C1' ATP sing 143 n n C2' H2' ATP sing 144 n n O2' HO2' ATP sing 145 n n C1' N9 ATP sing 146 n n C1' H1' ATP sing 147 n n N9 C8 ATP sing 148 n y N9 C4 ATP sing 149 n y C8 N7 ATP doub 150 n y C8 H8 ATP sing 151 n n N7 C5 ATP sing 152 n y C5 C6 ATP sing 153 n y C5 C4 ATP doub 154 n y C6 N6 ATP sing 155 n n C6 N1 ATP doub 156 n y N6 HN61 ATP sing 157 n n N6 HN62 ATP sing 158 n n N1 C2 ATP sing 159 n y C2 N3 ATP doub 160 n y C2 H2 ATP sing 161 n n N3 C4 ATP sing 162 n y # _atom_sites.entry_id 4Z1M _atom_sites.fract_transf_matrix[1][1] 0.009193 _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] 0.00644 _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] 0.00369 _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 K 5 ATP A 1 601 600 ATP ATP . L 6 MG A 1 602 601 MG MG . M 7 GOL A 1 603 4 GOL GOL . N 5 ATP B 1 601 600 ATP ATP . O 6 MG B 1 602 601 MG MG . P 8 CL B 1 603 10 CL CL . Q 7 GOL B 1 604 3 GOL GOL . R 5 ATP C 1 601 600 ATP ATP . S 6 MG C 1 602 601 MG MG . T 8 CL C 1 603 11 CL CL . U 8 CL C 1 604 13 CL CL . V 9 ADP D 1 600 600 ADP ADP . W 6 MG D 1 601 601 MG MG . X 8 CL E 1 501 1 CL CL . Y 8 CL E 1 502 2 CL CL . Z 8 CL E 1 503 7 CL CL . AA 8 CL E 1 504 12 CL CL . BA 9 ADP F 1 501 600 ADP ADP . CA 6 MG F 1 502 601 MG MG . DA 8 CL F 1 503 5 CL CL . EA 8 CL F 1 504 6 CL CL . FA 8 CL G 1 301 8 CL CL . GA 8 CL G 1 302 9 CL CL . HA 10 HOH A 1 701 42 HOH HOH . HA 10 HOH A 2 702 701 HOH HOH . HA 10 HOH A 3 703 703 HOH HOH . HA 10 HOH A 4 704 702 HOH HOH . IA 10 HOH B 1 701 703 HOH HOH . IA 10 HOH B 2 702 701 HOH HOH . IA 10 HOH B 3 703 702 HOH HOH . IA 10 HOH B 4 704 14 HOH HOH . JA 10 HOH C 1 701 43 HOH HOH . JA 10 HOH C 2 702 11 HOH HOH . JA 10 HOH C 3 703 702 HOH HOH . JA 10 HOH C 4 704 703 HOH HOH . JA 10 HOH C 5 705 701 HOH HOH . KA 10 HOH D 1 701 9 HOH HOH . KA 10 HOH D 2 702 701 HOH HOH . KA 10 HOH D 3 703 703 HOH HOH . KA 10 HOH D 4 704 702 HOH HOH . KA 10 HOH D 5 705 704 HOH HOH . LA 10 HOH E 1 601 23 HOH HOH . LA 10 HOH E 2 602 4 HOH HOH . LA 10 HOH E 3 603 13 HOH HOH . MA 10 HOH F 1 601 703 HOH HOH . MA 10 HOH F 2 602 701 HOH HOH . MA 10 HOH F 3 603 702 HOH HOH . MA 10 HOH F 4 604 704 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 PG ATP . . . N 5 52.879 -30.21 -32.579 1 54.49 ? PG ATP 601 B 1 HETATM 2 O O1G ATP . . . N 5 52.551 -28.758 -32.85 1 54.02 ? O1G ATP 601 B 1 HETATM 3 O O2G ATP . . . N 5 54.004 -30.416 -31.597 1 53.57 ? O2G ATP 601 B 1 HETATM 4 O O3G ATP . . . N 5 51.669 -31.071 -32.303 1 53.99 ? O3G ATP 601 B 1 HETATM 5 P PB ATP . . . N 5 54.628 -30.021 -34.796 1 55.01 ? PB ATP 601 B 1 HETATM 6 O O1B ATP . . . N 5 54.092 -28.7 -35.297 1 55.35 ? O1B ATP 601 B 1 HETATM 7 O O2B ATP . . . N 5 55.905 -30.042 -34.003 1 53.46 ? O2B ATP 601 B 1 HETATM 8 O O3B ATP . . . N 5 53.475 -30.786 -33.963 1 54.47 ? O3B ATP 601 B 1 HETATM 9 P PA ATP . . . N 5 55.737 -32.29 -36.007 1 55.77 ? PA ATP 601 B 1 HETATM 10 O O1A ATP . . . N 5 57.17 -31.858 -36.181 1 56.21 ? O1A ATP 601 B 1 HETATM 11 O O2A ATP . . . N 5 55.351 -33.085 -34.782 1 56.3 ? O2A ATP 601 B 1 HETATM 12 O O3A ATP . . . N 5 54.814 -30.978 -36.074 1 55.08 ? O3A ATP 601 B 1 HETATM 13 O O5' ATP . . . N 5 55.283 -33.081 -37.338 1 57.58 ? O5' ATP 601 B 1 HETATM 14 C C5' ATP . . . N 5 53.982 -33.657 -37.458 1 60.31 ? C5' ATP 601 B 1 HETATM 15 C C4' ATP . . . N 5 54.06 -35.028 -38.126 1 62.92 ? C4' ATP 601 B 1 HETATM 16 O O4' ATP . . . N 5 54.527 -34.885 -39.468 1 64.02 ? O4' ATP 601 B 1 HETATM 17 C C3' ATP . . . N 5 55.009 -35.982 -37.409 1 64.21 ? C3' ATP 601 B 1 HETATM 18 O O3' ATP . . . N 5 54.288 -37.113 -36.9 1 65.44 ? O3' ATP 601 B 1 HETATM 19 C C2' ATP . . . N 5 56.045 -36.397 -38.44 1 64.63 ? C2' ATP 601 B 1 HETATM 20 O O2' ATP . . . N 5 56.159 -37.822 -38.532 1 65.33 ? O2' ATP 601 B 1 HETATM 21 C C1' ATP . . . N 5 55.562 -35.825 -39.764 1 65.64 ? C1' ATP 601 B 1 HETATM 22 N N9 ATP . . . N 5 56.664 -35.15 -40.503 1 68.24 ? N9 ATP 601 B 1 HETATM 23 C C8 ATP . . . N 5 57.322 -34.039 -40.117 1 68.5 ? C8 ATP 601 B 1 HETATM 24 N N7 ATP . . . N 5 58.27 -33.686 -41.023 1 69.52 ? N7 ATP 601 B 1 HETATM 25 C C5 ATP . . . N 5 58.225 -34.582 -42.027 1 70.2 ? C5 ATP 601 B 1 HETATM 26 C C6 ATP . . . N 5 58.949 -34.803 -43.308 1 70.78 ? C6 ATP 601 B 1 HETATM 27 N N6 ATP . . . N 5 59.939 -33.969 -43.711 1 69.77 ? N6 ATP 601 B 1 HETATM 28 N N1 ATP . . . N 5 58.586 -35.867 -44.065 1 72.21 ? N1 ATP 601 B 1 HETATM 29 C C2 ATP . . . N 5 57.603 -36.711 -43.687 1 72.26 ? C2 ATP 601 B 1 HETATM 30 N N3 ATP . . . N 5 56.907 -36.57 -42.54 1 71.53 ? N3 ATP 601 B 1 HETATM 31 C C4 ATP . . . N 5 57.163 -35.545 -41.681 1 70.15 ? C4 ATP 601 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #