data_2VNP # _model_server_result.job_id VJUmC1YpYy-agC65vbvLWg _model_server_result.datetime_utc '2024-11-15 23:40:26' _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 2vnp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1182}' # _entry.id 2VNP # _exptl.entry_id 2VNP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 249.096 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-DIMETHYLAMINO-ETHYL-DIPHOSPHATE _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 100.3 _cell.angle_gamma 90 _cell.entry_id 2VNP _cell.length_a 43.2 _cell.length_b 69.1 _cell.length_c 62.4 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VNP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 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 monomeric 1 author_and_software_defined_assembly 1 PQS monomeric 1 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,C,D,E,I 1 1 B,F,G,H,J 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 ? 4 E N N ? 4 H 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 25 A HIS 25 1_555 C MN MN . A MN 1180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc2 A NE2 HIS 32 A HIS 32 1_555 C MN MN . A MN 1180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc3 A O CYS 67 A CYS 67 1_555 D MG MG . A MG 1181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc4 A NE2 HIS 69 A HIS 69 1_555 C MN MN . A MN 1180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc5 A OE2 GLU 87 A GLU 87 1_555 D MG MG . A MG 1181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc6 A OE1 GLU 114 A GLU 114 1_555 C MN MN . A MN 1180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc7 A OE2 GLU 114 A GLU 114 1_555 C MN MN . A MN 1180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? metalc ? metalc8 A OE2 GLU 116 A GLU 116 1_555 C MN MN . A MN 1180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc9 D MG MG . A MG 1181 1_555 E O6 DED . A DED 1182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc10 D MG MG . A MG 1181 1_555 E O2 DED . A DED 1182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc11 D MG MG . A MG 1181 1_555 I O HOH . A HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc12 D MG MG . A MG 1181 1_555 I O HOH . A HOH 2017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc13 B NE2 HIS 25 B HIS 25 1_555 F MN MN . B MN 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc14 B NE2 HIS 32 B HIS 32 1_555 F MN MN . B MN 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc15 B O CYS 67 B CYS 67 1_555 G MG MG . B MG 1185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc16 B NE2 HIS 69 B HIS 69 1_555 F MN MN . B MN 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc17 B OE2 GLU 87 B GLU 87 1_555 G MG MG . B MG 1185 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? metalc ? metalc18 B OE1 GLU 114 B GLU 114 1_555 F MN MN . B MN 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc19 B OE2 GLU 114 B GLU 114 1_555 F MN MN . B MN 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc20 B OE2 GLU 116 B GLU 116 1_555 F MN MN . B MN 1184 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.871 ? metalc ? metalc21 G MG MG . B MG 1185 1_555 H O1 DED . B DED 1186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc22 G MG MG . B MG 1185 1_555 H O6 DED . B DED 1186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc23 G MG MG . B MG 1185 1_555 J O HOH . B HOH 2015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc24 G MG MG . B MG 1185 1_555 J O HOH . B HOH 2025 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? # _chem_comp.formula 'C4 H13 N O7 P2' _chem_comp.formula_weight 249.096 _chem_comp.id DED _chem_comp.mon_nstd_flag . _chem_comp.name 2-DIMETHYLAMINO-ETHYL-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 O1 P4 DED sing 83 n n O1 HO1 DED sing 84 n n O2 P4 DED doub 85 n n O3 P4 DED sing 86 n n O3 HO3 DED sing 87 n n P4 O5 DED sing 88 n n O5 P8 DED sing 89 n n O6 P8 DED doub 90 n n O7 P8 DED sing 91 n n O7 HO7 DED sing 92 n n P8 O9 DED sing 93 n n O9 C10 DED sing 94 n n C10 C11 DED sing 95 n n C10 H101 DED sing 96 n n C10 H102 DED sing 97 n n C11 N12 DED sing 98 n n C11 H111 DED sing 99 n n C11 H112 DED sing 100 n n N12 C13 DED sing 101 n n N12 C14 DED sing 102 n n C13 H131 DED sing 103 n n C13 H132 DED sing 104 n n C13 H133 DED sing 105 n n C14 H141 DED sing 106 n n C14 H142 DED sing 107 n n C14 H143 DED sing 108 n n # _atom_sites.entry_id 2VNP _atom_sites.fract_transf_matrix[1][1] 0.023148 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004207 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014472 _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] 0.016288 _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 C 2 MN A 1 1180 1180 MN MN . D 3 MG A 1 1181 1181 MG MG . E 4 DED A 1 1182 1182 DED DED . F 2 MN B 1 1184 1184 MN MN . G 3 MG B 1 1185 1185 MG MG . H 4 DED B 1 1186 1186 DED DED . I 5 HOH A 1 2001 2001 HOH HOH . I 5 HOH A 2 2002 2002 HOH HOH . I 5 HOH A 3 2003 2003 HOH HOH . I 5 HOH A 4 2004 2004 HOH HOH . I 5 HOH A 5 2005 2005 HOH HOH . I 5 HOH A 6 2006 2006 HOH HOH . I 5 HOH A 7 2007 2007 HOH HOH . I 5 HOH A 8 2008 2008 HOH HOH . I 5 HOH A 9 2009 2009 HOH HOH . I 5 HOH A 10 2010 2010 HOH HOH . I 5 HOH A 11 2011 2011 HOH HOH . I 5 HOH A 12 2012 2012 HOH HOH . I 5 HOH A 13 2013 2013 HOH HOH . I 5 HOH A 14 2014 2014 HOH HOH . I 5 HOH A 15 2015 2015 HOH HOH . I 5 HOH A 16 2016 2016 HOH HOH . I 5 HOH A 17 2017 2017 HOH HOH . I 5 HOH A 18 2018 2018 HOH HOH . I 5 HOH A 19 2019 2019 HOH HOH . I 5 HOH A 20 2020 2020 HOH HOH . I 5 HOH A 21 2021 2021 HOH HOH . I 5 HOH A 22 2022 2022 HOH HOH . I 5 HOH A 23 2023 2023 HOH HOH . I 5 HOH A 24 2024 2024 HOH HOH . I 5 HOH A 25 2025 2025 HOH HOH . I 5 HOH A 26 2026 2026 HOH HOH . I 5 HOH A 27 2027 2027 HOH HOH . I 5 HOH A 28 2028 2028 HOH HOH . I 5 HOH A 29 2029 2029 HOH HOH . J 5 HOH B 1 2001 2001 HOH HOH . J 5 HOH B 2 2002 2002 HOH HOH . J 5 HOH B 3 2003 2003 HOH HOH . J 5 HOH B 4 2004 2004 HOH HOH . J 5 HOH B 5 2005 2005 HOH HOH . J 5 HOH B 6 2006 2006 HOH HOH . J 5 HOH B 7 2007 2007 HOH HOH . J 5 HOH B 8 2008 2008 HOH HOH . J 5 HOH B 9 2009 2009 HOH HOH . J 5 HOH B 10 2010 2010 HOH HOH . J 5 HOH B 11 2011 2011 HOH HOH . J 5 HOH B 12 2012 2012 HOH HOH . J 5 HOH B 13 2013 2013 HOH HOH . J 5 HOH B 14 2014 2014 HOH HOH . J 5 HOH B 15 2015 2015 HOH HOH . J 5 HOH B 16 2016 2016 HOH HOH . J 5 HOH B 17 2017 2017 HOH HOH . J 5 HOH B 18 2018 2018 HOH HOH . J 5 HOH B 19 2019 2019 HOH HOH . J 5 HOH B 20 2020 2020 HOH HOH . J 5 HOH B 21 2021 2021 HOH HOH . J 5 HOH B 22 2022 2022 HOH HOH . J 5 HOH B 23 2023 2023 HOH HOH . J 5 HOH B 24 2024 2024 HOH HOH . J 5 HOH B 25 2025 2025 HOH HOH . J 5 HOH B 26 2026 2026 HOH HOH . J 5 HOH B 27 2027 2027 HOH HOH . J 5 HOH B 28 2028 2028 HOH HOH . J 5 HOH B 29 2029 2029 HOH HOH . J 5 HOH B 30 2030 2030 HOH HOH . J 5 HOH B 31 2031 2031 HOH HOH . J 5 HOH B 32 2032 2032 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 O O1 DED . . . E 4 -1.672 0.625 21.387 1 25.62 ? O1 DED 1182 A 1 HETATM 2 O O2 DED . . . E 4 -3.721 1.069 19.963 1 26.76 ? O2 DED 1182 A 1 HETATM 3 O O3 DED . . . E 4 -1.547 0.295 18.909 1 27.37 ? O3 DED 1182 A 1 HETATM 4 P P4 DED . . . E 4 -2.438 0.267 20.093 1 27.07 ? P4 DED 1182 A 1 HETATM 5 O O5 DED . . . E 4 -2.733 -1.328 20.21 1 27.19 ? O5 DED 1182 A 1 HETATM 6 O O6 DED . . . E 4 -5.017 -1.514 19.203 1 28.26 ? O6 DED 1182 A 1 HETATM 7 O O7 DED . . . E 4 -3.05 -2.965 18.266 1 23.43 ? O7 DED 1182 A 1 HETATM 8 P P8 DED . . . E 4 -3.726 -2.3 19.389 1 23.7 ? P8 DED 1182 A 1 HETATM 9 O O9 DED . . . E 4 -4.054 -3.527 20.416 1 27.23 ? O9 DED 1182 A 1 HETATM 10 C C10 DED . . . E 4 -4.459 -3.401 21.815 1 22.22 ? C10 DED 1182 A 1 HETATM 11 C C11 DED . . . E 4 -4.404 -4.701 22.653 1 16.06 ? C11 DED 1182 A 1 HETATM 12 N N12 DED . . . E 4 -4.61 -5.926 21.822 1 17.31 ? N12 DED 1182 A 1 HETATM 13 C C13 DED . . . E 4 -5.897 -6.573 22.107 1 22.49 ? C13 DED 1182 A 1 HETATM 14 C C14 DED . . . E 4 -4.375 -5.928 20.375 1 20.26 ? C14 DED 1182 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 53 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #