data_7DDI # _model_server_result.job_id q1uKgtVWLLraA4UfldW22g _model_server_result.datetime_utc '2024-11-05 05:34:30' _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 7ddi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1102}' # _entry.id 7DDI # _exptl.entry_id 7DDI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 22.99 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SODIUM ION' _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 90 _cell.angle_gamma 90 _cell.entry_id 7DDI _cell.length_a 115.27 _cell.length_b 117.715 _cell.length_c 491.243 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DDI _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,B,C,G,H,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,JA 1 1 D,E,F,I,J,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,KA 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 ? 6 L N N ? 6 Z N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n G NAG 1 F 1 NAG B 1001 NAG 4 n G NAG 2 F 2 NAG B 1002 NAG 4 n H NAG 1 H 1 NAG B 1011 NAG 4 n H NAG 2 H 2 NAG B 1012 NAG 4 n I NAG 1 I 1 NAG D 1001 NAG 4 n I NAG 2 I 2 NAG D 1002 NAG 4 n J NAG 1 J 1 NAG D 1011 NAG 4 n J NAG 2 J 2 NAG D 1012 NAG # 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 disulf ? disulf1 B SG CYS 126 B CYS 126 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 B SG CYS 159 B CYS 159 1_555 B SG CYS 175 B CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 B SG CYS 213 B CYS 213 1_555 B SG CYS 276 B CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 E SG CYS 126 D CYS 126 1_555 E SG CYS 149 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 E SG CYS 159 D CYS 159 1_555 E SG CYS 175 D CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf6 E SG CYS 213 D CYS 213 1_555 E SG CYS 276 D CYS 276 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A C SER 368 A SER 368 1_555 A N PHD 369 A PHD 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale2 A C PHD 369 A PHD 369 1_555 A N LYS 370 A LYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 B ND2 ASN 158 B ASN 158 1_555 G C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 B ND2 ASN 193 B ASN 193 1_555 W C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 B ND2 ASN 265 B ASN 265 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 D C SER 368 C SER 368 1_555 D N PHD 369 C PHD 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 D C PHD 369 C PHD 369 1_555 D N LYS 370 C LYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale8 E ND2 ASN 158 D ASN 158 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale9 E ND2 ASN 193 D ASN 193 1_555 GA C1 NAG . D NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale10 E ND2 ASN 265 D ASN 265 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 G O4 NAG . F NAG 1 1_555 G C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale12 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale13 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale14 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? metalc ? metalc1 A OE2 GLU 327 A GLU 327 1_555 M MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc2 A OD2 PHD 369 A PHD 369 1_555 K MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc3 A OP3 PHD 369 A PHD 369 1_555 K MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc4 A O THR 371 A THR 371 1_555 K MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc5 A OD1 ASP 710 A ASP 710 1_555 K MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc6 A OD2 ASP 710 A ASP 710 1_555 K MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc7 A OD1 ASP 740 A ASP 740 1_555 L NA NA . A NA 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc8 A OD2 ASP 740 A ASP 740 1_555 L NA NA . A NA 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc9 A OE2 GLU 779 A GLU 779 1_555 M MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc10 A OD1 ASP 804 A ASP 804 1_555 M MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc11 A OD2 ASP 804 A ASP 804 1_555 M MG MG . A MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc12 K MG MG . A MG 1101 1_555 JA O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc13 K MG MG . A MG 1101 1_555 JA O HOH . A HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc14 M MG MG . A MG 1103 1_555 JA O HOH . A HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc15 M MG MG . A MG 1103 1_555 JA O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc16 M MG MG . A MG 1103 1_555 JA O HOH . A HOH 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc17 D OE2 GLU 327 C GLU 327 1_555 AA MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc18 D OD2 PHD 369 C PHD 369 1_555 Y MG MG . C MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc19 D OP3 PHD 369 C PHD 369 1_555 Y MG MG . C MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc20 D O THR 371 C THR 371 1_555 Y MG MG . C MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc21 D OD1 ASP 710 C ASP 710 1_555 Y MG MG . C MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc22 D OD2 ASP 710 C ASP 710 1_555 Y MG MG . C MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc23 D OD1 ASP 740 C ASP 740 1_555 Z NA NA . C NA 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.052 ? metalc ? metalc24 D OD2 ASP 740 C ASP 740 1_555 Z NA NA . C NA 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc25 D OE2 GLU 779 C GLU 779 1_555 AA MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc26 D OD1 ASP 804 C ASP 804 1_555 AA MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc27 D OD2 ASP 804 C ASP 804 1_555 AA MG MG . C MG 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc28 Y MG MG . C MG 1101 1_555 KA O HOH . C HOH 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc29 Y MG MG . C MG 1101 1_555 KA O HOH . C HOH 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc30 AA MG MG . C MG 1103 1_555 KA O HOH . C HOH 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc31 AA MG MG . C MG 1103 1_555 KA O HOH . C HOH 1204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc32 AA MG MG . C MG 1103 1_555 KA O HOH . C HOH 1205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? # _chem_comp.formula 'Na 1' _chem_comp.formula_weight 22.99 _chem_comp.id NA _chem_comp.mon_nstd_flag . _chem_comp.name 'SODIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 7DDI _atom_sites.fract_transf_matrix[1][1] 0.008675 _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] 0.008495 _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] 0.002036 _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 MG A 1 1101 1101 MG MG . L 6 NA A 1 1102 1102 NA NA . M 5 MG A 1 1103 1103 MG MG . N 7 PCW A 1 1110 1202 PCW PCW . O 7 PCW A 1 1105 1203 PCW PCW . P 7 PCW A 1 1106 1204 PCW PCW . Q 7 PCW A 1 1107 1208 PCW PCW . R 7 PCW A 1 1108 1212 PCW PCW . S 7 PCW A 1 1109 1215 PCW PCW . T 8 F9R A 1 1121 3000 F9R DTX . U 9 CLR A 1 1111 1107 CLR CLR . V 7 PCW A 1 1112 1215 PCW PCW . W 10 NAG B 1 401 1021 NAG NAG . X 9 CLR G 1 101 1106 CLR CLR . Y 5 MG C 1 1101 1101 MG MG . Z 6 NA C 1 1102 1102 NA NA . AA 5 MG C 1 1103 1103 MG MG . BA 9 CLR C 1 1104 1107 CLR CLR . CA 7 PCW C 1 1105 1203 PCW PCW . DA 7 PCW C 1 1106 1205 PCW PCW . EA 7 PCW C 1 1107 1207 PCW PCW . FA 8 F9R C 1 1121 3000 F9R DTX . GA 10 NAG D 1 401 1021 NAG NAG . HA 7 PCW D 1 402 1205 PCW PCW . IA 9 CLR E 1 101 1106 CLR CLR . JA 11 HOH A 1 2001 2001 HOH HOH . JA 11 HOH A 2 2002 2114 HOH HOH . JA 11 HOH A 3 2003 2105 HOH HOH . JA 11 HOH A 4 2004 2003 HOH HOH . JA 11 HOH A 5 2005 2004 HOH HOH . KA 11 HOH C 1 1201 2114 HOH HOH . KA 11 HOH C 2 1202 2105 HOH HOH . KA 11 HOH C 3 1203 2003 HOH HOH . KA 11 HOH C 4 1204 2001 HOH HOH . KA 11 HOH C 5 1205 2004 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NA _atom_site.label_atom_id NA _atom_site.label_comp_id NA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id L _atom_site.label_entity_id 6 _atom_site.Cartn_x 7.241 _atom_site.Cartn_y -29.62 _atom_site.Cartn_z 92.51 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 104.17 _atom_site.pdbx_formal_charge 1 _atom_site.auth_atom_id NA _atom_site.auth_comp_id NA _atom_site.auth_seq_id 1102 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 39 _model_server_stats.query_time_ms 345 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #