data_1MKD # _model_server_result.job_id '_gTel9zBvSHE44PdO_QpeA' _model_server_result.datetime_utc '2024-10-18 16:28:44' _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 1mkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"CA","auth_seq_id":2012}' # _entry.id 1MKD # _exptl.entry_id 1MKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 24.305 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MAGNESIUM ION' _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 1MKD _cell.length_a 97.325 _cell.length_b 164.572 _cell.length_c 325.54 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? hexameric 6 author_defined_assembly 1 ? hexameric 6 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,B,E,H,I,J,M,N,O,P,Q,R,Y,Z,AA,HA,IA,JA,KA,LA,MA,NA,OA,PA,WA,XA,AB,DB,EB,FB 1 1 C,D,F,G,K,L,S,T,U,V,W,X,BA,CA,DA,EA,FA,GA,QA,RA,SA,TA,UA,VA,YA,ZA,BB,CB,GB,HB 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 Q N N ? 3 T N N ? 3 W N N ? 3 Z N N ? 3 CA N N ? 3 FA N N ? 3 IA N N ? 3 LA N N ? 3 OA N N ? 3 RA N N ? 3 UA 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 NE2 HIS 79 A HIS 261 1_555 M ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc2 A NE2 HIS 115 A HIS 297 1_555 M ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc3 A OD2 ASP 116 A ASP 298 1_555 M ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc4 A OD1 ASP 116 A ASP 298 1_555 N MG MG . A MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc5 A OD1 ASP 233 A ASP 415 1_555 M ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc6 B NE2 HIS 79 B HIS 261 1_555 P ZN ZN . B ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc7 B NE2 HIS 115 B HIS 297 1_555 P ZN ZN . B ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc8 B OD2 ASP 116 B ASP 298 1_555 P ZN ZN . B ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc9 B OD1 ASP 116 B ASP 298 1_555 Q MG MG . B MG 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc10 B OD1 ASP 233 B ASP 415 1_555 P ZN ZN . B ZN 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc11 C NE2 HIS 79 C HIS 261 1_555 S ZN ZN . C ZN 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc12 C NE2 HIS 115 C HIS 297 1_555 S ZN ZN . C ZN 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc13 C OD2 ASP 116 C ASP 298 1_555 S ZN ZN . C ZN 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc14 C OD1 ASP 116 C ASP 298 1_555 T MG MG . C MG 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc15 C OD1 ASP 233 C ASP 415 1_555 S ZN ZN . C ZN 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc16 D NE2 HIS 79 D HIS 261 1_555 V ZN ZN . D ZN 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc17 D NE2 HIS 115 D HIS 297 1_555 V ZN ZN . D ZN 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc18 D OD2 ASP 116 D ASP 298 1_555 V ZN ZN . D ZN 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? metalc ? metalc19 D OD1 ASP 116 D ASP 298 1_555 W MG MG . D MG 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc20 D OD1 ASP 233 D ASP 415 1_555 V ZN ZN . D ZN 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc21 E NE2 HIS 79 E HIS 261 1_555 Y ZN ZN . E ZN 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc22 E NE2 HIS 115 E HIS 297 1_555 Y ZN ZN . E ZN 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc23 E OD2 ASP 116 E ASP 298 1_555 Y ZN ZN . E ZN 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc24 E OD1 ASP 116 E ASP 298 1_555 Z MG MG . E MG 2010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc25 E OD1 ASP 233 E ASP 415 1_555 Y ZN ZN . E ZN 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc26 F NE2 HIS 79 F HIS 261 1_555 BA ZN ZN . F ZN 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc27 F NE2 HIS 115 F HIS 297 1_555 BA ZN ZN . F ZN 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc28 F OD2 ASP 116 F ASP 298 1_555 BA ZN ZN . F ZN 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc29 F OD1 ASP 116 F ASP 298 1_555 CA MG MG . F MG 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc30 F OD1 ASP 233 F ASP 415 1_555 BA ZN ZN . F ZN 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc31 G NE2 HIS 79 G HIS 261 1_555 EA ZN ZN . G ZN 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc32 G NE2 HIS 115 G HIS 297 1_555 EA ZN ZN . G ZN 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc33 G OD2 ASP 116 G ASP 298 1_555 EA ZN ZN . G ZN 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc34 G OD1 ASP 116 G ASP 298 1_555 FA MG MG . G MG 2014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc35 G OD1 ASP 233 G ASP 415 1_555 EA ZN ZN . G ZN 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc36 H NE2 HIS 79 H HIS 261 1_555 HA ZN ZN . H ZN 2015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc37 H NE2 HIS 115 H HIS 297 1_555 HA ZN ZN . H ZN 2015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc38 H OD2 ASP 116 H ASP 298 1_555 HA ZN ZN . H ZN 2015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc39 H OD1 ASP 116 H ASP 298 1_555 IA MG MG . H MG 2016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc40 H OD1 ASP 233 H ASP 415 1_555 HA ZN ZN . H ZN 2015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc41 I NE2 HIS 79 I HIS 261 1_555 KA ZN ZN . I ZN 2017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc42 I NE2 HIS 115 I HIS 297 1_555 KA ZN ZN . I ZN 2017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc43 I OD2 ASP 116 I ASP 298 1_555 KA ZN ZN . I ZN 2017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc44 I OD1 ASP 116 I ASP 298 1_555 LA MG MG . I MG 2018 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc45 I OD1 ASP 233 I ASP 415 1_555 KA ZN ZN . I ZN 2017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc46 J NE2 HIS 79 J HIS 261 1_555 NA ZN ZN . J ZN 2019 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc47 J NE2 HIS 115 J HIS 297 1_555 NA ZN ZN . J ZN 2019 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc48 J OD2 ASP 116 J ASP 298 1_555 NA ZN ZN . J ZN 2019 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc49 J OD1 ASP 116 J ASP 298 1_555 OA MG MG . J MG 2020 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc50 J OD1 ASP 233 J ASP 415 1_555 NA ZN ZN . J ZN 2019 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc51 K NE2 HIS 79 K HIS 261 1_555 QA ZN ZN . K ZN 2021 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc52 K NE2 HIS 115 K HIS 297 1_555 QA ZN ZN . K ZN 2021 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc53 K OD2 ASP 116 K ASP 298 1_555 QA ZN ZN . K ZN 2021 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc54 K OD1 ASP 116 K ASP 298 1_555 RA MG MG . K MG 2022 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc55 K OD1 ASP 233 K ASP 415 1_555 QA ZN ZN . K ZN 2021 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc56 L NE2 HIS 79 L HIS 261 1_555 TA ZN ZN . L ZN 2023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc57 L NE2 HIS 115 L HIS 297 1_555 TA ZN ZN . L ZN 2023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc58 L OD2 ASP 116 L ASP 298 1_555 TA ZN ZN . L ZN 2023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc59 L OD1 ASP 116 L ASP 298 1_555 UA MG MG . L MG 2024 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc60 L OD1 ASP 233 L ASP 415 1_555 TA ZN ZN . L ZN 2023 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? # _chem_comp.formula 'Mg 2' _chem_comp.formula_weight 24.305 _chem_comp.id MG _chem_comp.mon_nstd_flag . _chem_comp.name 'MAGNESIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1MKD _atom_sites.fract_transf_matrix[1][1] 0.010275 _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] 0.006076 _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] 0.003072 _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 ZN A 1 2001 2001 ZN ZN2 . N 3 MG A 1 2002 2002 MG MG2 . O 4 ZAR A 1 3001 3001 ZAR ZAR . P 2 ZN B 1 2003 2003 ZN ZN2 . Q 3 MG B 1 2004 2004 MG MG2 . R 4 ZAR B 1 3002 3002 ZAR ZAR . S 2 ZN C 1 2005 2005 ZN ZN2 . T 3 MG C 1 2006 2006 MG MG2 . U 4 ZAR C 1 3003 3003 ZAR ZAR . V 2 ZN D 1 2007 2007 ZN ZN2 . W 3 MG D 1 2008 2008 MG MG2 . X 4 ZAR D 1 3004 3004 ZAR ZAR . Y 2 ZN E 1 2009 2009 ZN ZN2 . Z 3 MG E 1 2010 2010 MG MG2 . AA 4 ZAR E 1 3005 3005 ZAR ZAR . BA 2 ZN F 1 2011 2011 ZN ZN2 . CA 3 MG F 1 2012 2012 MG MG2 . DA 4 ZAR F 1 3006 3006 ZAR ZAR . EA 2 ZN G 1 2013 2013 ZN ZN2 . FA 3 MG G 1 2014 2014 MG MG2 . GA 4 ZAR G 1 3007 3007 ZAR ZAR . HA 2 ZN H 1 2015 2015 ZN ZN2 . IA 3 MG H 1 2016 2016 MG MG2 . JA 4 ZAR H 1 3008 3008 ZAR ZAR . KA 2 ZN I 1 2017 2017 ZN ZN2 . LA 3 MG I 1 2018 2018 MG MG2 . MA 4 ZAR I 1 3009 3009 ZAR ZAR . NA 2 ZN J 1 2019 2019 ZN ZN2 . OA 3 MG J 1 2020 2020 MG MG2 . PA 4 ZAR J 1 3010 3010 ZAR ZAR . QA 2 ZN K 1 2021 2021 ZN ZN2 . RA 3 MG K 1 2022 2022 MG MG2 . SA 4 ZAR K 1 3011 3011 ZAR ZAR . TA 2 ZN L 1 2023 2023 ZN ZN2 . UA 3 MG L 1 2024 2024 MG MG2 . VA 4 ZAR L 1 3012 3012 ZAR ZAR . WA 5 HOH A 1 1001 1001 HOH TIP . XA 5 HOH B 1 1002 1002 HOH TIP . YA 5 HOH C 1 1003 1003 HOH TIP . ZA 5 HOH D 1 1004 1004 HOH TIP . AB 5 HOH E 1 1005 1005 HOH TIP . BB 5 HOH F 1 1006 1006 HOH TIP . CB 5 HOH G 1 1007 1007 HOH TIP . DB 5 HOH H 1 1008 1008 HOH TIP . EB 5 HOH I 1 1009 1009 HOH TIP . FB 5 HOH J 1 1010 1010 HOH TIP . GB 5 HOH K 1 1011 1011 HOH TIP . HB 5 HOH L 1 1012 1012 HOH TIP . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MG _atom_site.label_atom_id MG _atom_site.label_comp_id MG _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id CA _atom_site.label_entity_id 3 _atom_site.Cartn_x 62.737 _atom_site.Cartn_y -27.787 _atom_site.Cartn_z 32.807 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 25.93 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MG _atom_site.auth_comp_id MG _atom_site.auth_seq_id 2012 _atom_site.auth_asym_id F _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #