data_2VKD # _model_server_result.job_id b7W3JzLuMIvUvfy6nDAP6g _model_server_result.datetime_utc '2024-11-12 19:44:02' _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 2vkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1552}' # _entry.id 2VKD # _exptl.entry_id 2VKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 54.938 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'MANGANESE (II) ION' _entity.pdbx_number_of_molecules 5 _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 2VKD _cell.length_a 57.287 _cell.length_b 190.322 _cell.length_c 204.419 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VKD _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 PQS monomeric 1 author_and_software_defined_assembly 1 PQS monomeric 1 author_and_software_defined_assembly 2 PQS monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,L 1 1 B,H,I,M 2 1 C,J,K,N 3 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 ? 2 D N N ? 2 F N N ? 2 G N N ? 2 H N N ? 2 J 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 OD1 ASP 280 A ASP 280 1_555 F MN MN . A MN 1551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc2 A OD2 ASP 288 A ASP 288 1_555 D MN MN . A MN 1543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc3 A OE1 GLU 515 A GLU 515 1_555 D MN MN . A MN 1543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc4 D MN MN . A MN 1543 1_555 E O1B UPG . A UPG 1544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc5 D MN MN . A MN 1543 1_555 E O1A UPG . A UPG 1544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.841 ? metalc ? metalc6 D MN MN . A MN 1543 1_555 L O HOH . A HOH 2046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc7 D MN MN . A MN 1543 1_555 L O HOH . A HOH 2047 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc8 F MN MN . A MN 1551 1_555 B OE2 GLU 219 B GLU 219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc9 G MN MN . A MN 1552 1_555 C OD1 ASP 280 C ASP 280 3_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc10 B OD2 ASP 288 B ASP 288 1_555 H MN MN . B MN 1541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc11 B OE1 GLU 515 B GLU 515 1_555 H MN MN . B MN 1541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc12 H MN MN . B MN 1541 1_555 I O1B UPG . B UPG 1544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc13 H MN MN . B MN 1541 1_555 I O1A UPG . B UPG 1544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc14 C OD2 ASP 288 C ASP 288 1_555 J MN MN . C MN 1542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc15 C OE1 GLU 515 C GLU 515 1_555 J MN MN . C MN 1542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc16 J MN MN . C MN 1542 1_555 K O1B UPG . C UPG 1544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc17 J MN MN . C MN 1542 1_555 K O1A UPG . C UPG 1544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc18 J MN MN . C MN 1542 1_555 N O HOH . C HOH 2044 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? # _chem_comp.formula 'Mn 2' _chem_comp.formula_weight 54.938 _chem_comp.id MN _chem_comp.mon_nstd_flag . _chem_comp.name 'MANGANESE (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2VKD _atom_sites.fract_transf_matrix[1][1] 0.017456 _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] 0.005254 _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] 0.004892 _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 D 2 MN A 1 1543 1543 MN MN . E 3 UPG A 1 1544 1544 UPG UPG . F 2 MN A 1 1551 1551 MN MN . G 2 MN A 1 1552 1552 MN MN . H 2 MN B 1 1541 1541 MN MN . I 3 UPG B 1 1544 1544 UPG UPG . J 2 MN C 1 1542 1542 MN MN . K 3 UPG C 1 1544 1544 UPG UPG . L 4 HOH A 1 2001 2001 HOH HOH . L 4 HOH A 2 2002 2002 HOH HOH . L 4 HOH A 3 2003 2003 HOH HOH . L 4 HOH A 4 2004 2004 HOH HOH . L 4 HOH A 5 2005 2005 HOH HOH . L 4 HOH A 6 2006 2006 HOH HOH . L 4 HOH A 7 2007 2007 HOH HOH . L 4 HOH A 8 2008 2008 HOH HOH . L 4 HOH A 9 2009 2009 HOH HOH . L 4 HOH A 10 2010 2010 HOH HOH . L 4 HOH A 11 2011 2011 HOH HOH . L 4 HOH A 12 2012 2012 HOH HOH . L 4 HOH A 13 2013 2013 HOH HOH . L 4 HOH A 14 2014 2014 HOH HOH . L 4 HOH A 15 2015 2015 HOH HOH . L 4 HOH A 16 2016 2016 HOH HOH . L 4 HOH A 17 2017 2017 HOH HOH . L 4 HOH A 18 2018 2018 HOH HOH . L 4 HOH A 19 2019 2019 HOH HOH . L 4 HOH A 20 2020 2020 HOH HOH . L 4 HOH A 21 2021 2021 HOH HOH . L 4 HOH A 22 2022 2022 HOH HOH . L 4 HOH A 23 2023 2023 HOH HOH . L 4 HOH A 24 2024 2024 HOH HOH . L 4 HOH A 25 2025 2025 HOH HOH . L 4 HOH A 26 2026 2026 HOH HOH . L 4 HOH A 27 2027 2027 HOH HOH . L 4 HOH A 28 2028 2028 HOH HOH . L 4 HOH A 29 2029 2029 HOH HOH . L 4 HOH A 30 2030 2030 HOH HOH . L 4 HOH A 31 2031 2031 HOH HOH . L 4 HOH A 32 2032 2032 HOH HOH . L 4 HOH A 33 2033 2033 HOH HOH . L 4 HOH A 34 2034 2034 HOH HOH . L 4 HOH A 35 2035 2035 HOH HOH . L 4 HOH A 36 2036 2036 HOH HOH . L 4 HOH A 37 2037 2037 HOH HOH . L 4 HOH A 38 2038 2038 HOH HOH . L 4 HOH A 39 2039 2039 HOH HOH . L 4 HOH A 40 2040 2040 HOH HOH . L 4 HOH A 41 2041 2041 HOH HOH . L 4 HOH A 42 2042 2042 HOH HOH . L 4 HOH A 43 2043 2043 HOH HOH . L 4 HOH A 44 2044 2044 HOH HOH . L 4 HOH A 45 2045 2045 HOH HOH . L 4 HOH A 46 2046 2046 HOH HOH . L 4 HOH A 47 2047 2047 HOH HOH . M 4 HOH B 1 2001 2001 HOH HOH . M 4 HOH B 2 2002 2002 HOH HOH . M 4 HOH B 3 2003 2003 HOH HOH . M 4 HOH B 4 2004 2004 HOH HOH . M 4 HOH B 5 2005 2005 HOH HOH . M 4 HOH B 6 2006 2006 HOH HOH . M 4 HOH B 7 2007 2007 HOH HOH . M 4 HOH B 8 2008 2008 HOH HOH . M 4 HOH B 9 2009 2009 HOH HOH . M 4 HOH B 10 2010 2010 HOH HOH . M 4 HOH B 11 2011 2011 HOH HOH . M 4 HOH B 12 2012 2012 HOH HOH . M 4 HOH B 13 2013 2013 HOH HOH . M 4 HOH B 14 2014 2014 HOH HOH . M 4 HOH B 15 2015 2015 HOH HOH . M 4 HOH B 16 2016 2016 HOH HOH . M 4 HOH B 17 2017 2017 HOH HOH . M 4 HOH B 18 2018 2018 HOH HOH . M 4 HOH B 19 2019 2019 HOH HOH . M 4 HOH B 20 2020 2020 HOH HOH . M 4 HOH B 21 2021 2021 HOH HOH . M 4 HOH B 22 2022 2022 HOH HOH . M 4 HOH B 23 2023 2023 HOH HOH . M 4 HOH B 24 2024 2024 HOH HOH . M 4 HOH B 25 2025 2025 HOH HOH . M 4 HOH B 26 2026 2026 HOH HOH . M 4 HOH B 27 2027 2027 HOH HOH . M 4 HOH B 28 2028 2028 HOH HOH . M 4 HOH B 29 2029 2029 HOH HOH . M 4 HOH B 30 2030 2030 HOH HOH . M 4 HOH B 31 2031 2031 HOH HOH . M 4 HOH B 32 2032 2032 HOH HOH . M 4 HOH B 33 2033 2033 HOH HOH . M 4 HOH B 34 2034 2034 HOH HOH . M 4 HOH B 35 2035 2035 HOH HOH . M 4 HOH B 36 2036 2036 HOH HOH . M 4 HOH B 37 2037 2037 HOH HOH . M 4 HOH B 38 2038 2038 HOH HOH . M 4 HOH B 39 2039 2039 HOH HOH . M 4 HOH B 40 2040 2040 HOH HOH . M 4 HOH B 41 2041 2041 HOH HOH . M 4 HOH B 42 2042 2042 HOH HOH . M 4 HOH B 43 2043 2043 HOH HOH . M 4 HOH B 44 2044 2044 HOH HOH . M 4 HOH B 45 2045 2045 HOH HOH . M 4 HOH B 46 2046 2046 HOH HOH . M 4 HOH B 47 2047 2047 HOH HOH . M 4 HOH B 48 2048 2048 HOH HOH . M 4 HOH B 49 2049 2049 HOH HOH . M 4 HOH B 50 2050 2050 HOH HOH . M 4 HOH B 51 2051 2051 HOH HOH . M 4 HOH B 52 2052 2052 HOH HOH . M 4 HOH B 53 2053 2053 HOH HOH . M 4 HOH B 54 2054 2054 HOH HOH . M 4 HOH B 55 2055 2055 HOH HOH . M 4 HOH B 56 2056 2056 HOH HOH . M 4 HOH B 57 2057 2057 HOH HOH . N 4 HOH C 1 2001 2001 HOH HOH . N 4 HOH C 2 2002 2002 HOH HOH . N 4 HOH C 3 2003 2003 HOH HOH . N 4 HOH C 4 2004 2004 HOH HOH . N 4 HOH C 5 2005 2005 HOH HOH . N 4 HOH C 6 2006 2006 HOH HOH . N 4 HOH C 7 2007 2007 HOH HOH . N 4 HOH C 8 2008 2008 HOH HOH . N 4 HOH C 9 2009 2009 HOH HOH . N 4 HOH C 10 2010 2010 HOH HOH . N 4 HOH C 11 2011 2011 HOH HOH . N 4 HOH C 12 2012 2012 HOH HOH . N 4 HOH C 13 2013 2013 HOH HOH . N 4 HOH C 14 2014 2014 HOH HOH . N 4 HOH C 15 2015 2015 HOH HOH . N 4 HOH C 16 2016 2016 HOH HOH . N 4 HOH C 17 2017 2017 HOH HOH . N 4 HOH C 18 2018 2018 HOH HOH . N 4 HOH C 19 2019 2019 HOH HOH . N 4 HOH C 20 2020 2020 HOH HOH . N 4 HOH C 21 2021 2021 HOH HOH . N 4 HOH C 22 2022 2022 HOH HOH . N 4 HOH C 23 2023 2023 HOH HOH . N 4 HOH C 24 2024 2024 HOH HOH . N 4 HOH C 25 2025 2025 HOH HOH . N 4 HOH C 26 2026 2026 HOH HOH . N 4 HOH C 27 2027 2027 HOH HOH . N 4 HOH C 28 2028 2028 HOH HOH . N 4 HOH C 29 2029 2029 HOH HOH . N 4 HOH C 30 2030 2030 HOH HOH . N 4 HOH C 31 2031 2031 HOH HOH . N 4 HOH C 32 2032 2032 HOH HOH . N 4 HOH C 33 2033 2033 HOH HOH . N 4 HOH C 34 2034 2034 HOH HOH . N 4 HOH C 35 2035 2035 HOH HOH . N 4 HOH C 36 2036 2036 HOH HOH . N 4 HOH C 37 2037 2037 HOH HOH . N 4 HOH C 38 2038 2038 HOH HOH . N 4 HOH C 39 2039 2039 HOH HOH . N 4 HOH C 40 2040 2040 HOH HOH . N 4 HOH C 41 2041 2041 HOH HOH . N 4 HOH C 42 2042 2042 HOH HOH . N 4 HOH C 43 2043 2043 HOH HOH . N 4 HOH C 44 2044 2044 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol MN _atom_site.label_atom_id MN _atom_site.label_comp_id MN _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id G _atom_site.label_entity_id 2 _atom_site.Cartn_x 20.826 _atom_site.Cartn_y 47.588 _atom_site.Cartn_z 58.083 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 63.74 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id MN _atom_site.auth_comp_id MN _atom_site.auth_seq_id 1552 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #