data_6LKN # _model_server_result.job_id 5PKV04odEBUOdJRHXR-Mcw _model_server_result.datetime_utc '2024-12-12 11:00:05' _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 6lkn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":403}' # _entry.id 6LKN # _exptl.entry_id 6LKN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 164.156 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 1-deoxy-alpha-D-mannopyranose _entity.pdbx_number_of_molecules 4 _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 6LKN _cell.length_a 100.46 _cell.length_b 232.83 _cell.length_c 492.89 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LKN _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,K,L,M,N,O,P,NA 1 1 C,D,Q,R,S,T,U,V,W,X,OA 2 1 E,F,Y,Z,AA,BA,CA,DA,EA,FA,PA 3 1 G,H,GA,HA,IA,JA,KA,LA,MA,QA 4 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 N N N ? 6 V N N ? 6 DA N N ? 6 KA 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 disulf ? disulf1 B SG CYS 91 C CYS 91 1_555 B SG CYS 104 C CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 B SG CYS 94 C CYS 94 1_555 B SG CYS 102 C CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 C SG CYS 165 E CYS 165 1_555 C SG CYS 197 E CYS 197 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? disulf ? disulf4 D SG CYS 94 F CYS 94 1_555 D SG CYS 102 F CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 F SG CYS 91 J CYS 91 1_555 F SG CYS 104 J CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 F SG CYS 94 J CYS 94 1_555 F SG CYS 102 J CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 H SG CYS 91 N CYS 91 1_555 H SG CYS 104 N CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? disulf ? disulf8 H SG CYS 94 N CYS 94 1_555 H SG CYS 102 N CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A C THR 408 A THR 408 1_555 A N BFD 409 A BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C BFD 409 A BFD 409 1_555 A N LYS 410 A LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 C C THR 408 E THR 408 1_555 C N BFD 409 E BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 C C BFD 409 E BFD 409 1_555 C N LYS 410 E LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale5 E C THR 408 I THR 408 1_555 E N BFD 409 I BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 E C BFD 409 I BFD 409 1_555 E N LYS 410 I LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 G C THR 408 M THR 408 1_555 G N BFD 409 M BFD 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale8 G C BFD 409 M BFD 409 1_555 G N LYS 410 M LYS 410 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OD2 BFD 409 A BFD 409 1_555 J MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.685 ? metalc ? metalc2 A OD1 ASP 816 A ASP 816 1_555 J MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc3 A OD1 ASP 820 A ASP 820 1_555 J MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.943 ? metalc ? metalc4 J MG MG . A MG 1202 1_555 NA O HOH . A HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc5 J MG MG . A MG 1202 1_555 NA O HOH . A HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc6 S MG MG . E MG 1203 1_555 OA O HOH . E HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc7 S MG MG . E MG 1203 1_555 OA O HOH . E HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc8 E O THR 411 I THR 411 1_555 AA MG MG . I MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc9 E OD1 ASP 816 I ASP 816 1_555 AA MG MG . I MG 1203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc10 AA MG MG . I MG 1203 1_555 PA O HOH . I HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc11 AA MG MG . I MG 1203 1_555 PA O HOH . I HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc12 G OG1 THR 413 M THR 413 1_555 HA MG MG . M MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? metalc ? metalc13 G OD2 ASP 816 M ASP 816 1_555 HA MG MG . M MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc14 HA MG MG . M MG 1202 1_555 QA O HOH . M HOH 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc15 HA MG MG . M MG 1202 1_555 QA O HOH . M HOH 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? # _chem_comp.formula 'C6 H12 O5' _chem_comp.formula_weight 164.156 _chem_comp.id AH2 _chem_comp.mon_nstd_flag . _chem_comp.name 1-deoxy-alpha-D-mannopyranose _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 1,5-Anhydromannitol;1-deoxy-alpha-D-mannose;1-deoxy-D-mannose;1-deoxy-mannose # 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 C1 O5 AH2 sing 1 n n C1 C2 AH2 sing 2 n n O5 C5 AH2 sing 3 n n C2 C3 AH2 sing 4 n n C2 O2 AH2 sing 5 n n C5 C6 AH2 sing 6 n n C5 C4 AH2 sing 7 n n C3 C4 AH2 sing 8 n n C3 O3 AH2 sing 9 n n C6 O6 AH2 sing 10 n n C4 O4 AH2 sing 11 n n O3 HO3 AH2 sing 12 n n C4 H4 AH2 sing 13 n n C5 H5 AH2 sing 14 n n O4 HO4 AH2 sing 15 n n C6 H61 AH2 sing 16 n n C6 H62 AH2 sing 17 n n O6 HO6 AH2 sing 18 n n C3 H3 AH2 sing 19 n n C2 H2 AH2 sing 20 n n O2 HO2 AH2 sing 21 n n C1 H1 AH2 sing 22 n n C1 H11 AH2 sing 23 n n # _atom_sites.entry_id 6LKN _atom_sites.fract_transf_matrix[1][1] 0.009954 _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] 0.004295 _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] 0.002029 _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 I 3 P5S A 1 1201 2000 P5S P5S . J 4 MG A 1 1202 2002 MG MO6 . K 3 P5S C 1 401 1999 P5S P5S . L 5 NAG C 1 402 401 NAG NAG . M 5 NAG C 1 403 402 NAG NAG . N 6 AH2 C 1 404 403 AH2 MAN . O 5 NAG C 1 405 404 NAG NAG . P 5 NAG C 1 406 405 NAG NAG . Q 3 P5S E 1 1201 1999 P5S P5S . R 3 P5S E 1 1202 2000 P5S P5S . S 4 MG E 1 1203 2002 MG MO6 . T 5 NAG F 1 401 401 NAG NAG . U 5 NAG F 1 402 402 NAG NAG . V 6 AH2 F 1 403 403 AH2 MAN . W 5 NAG F 1 404 404 NAG NAG . X 5 NAG F 1 405 405 NAG NAG . Y 3 P5S I 1 1201 1999 P5S P5S . Z 3 P5S I 1 1202 2000 P5S P5S . AA 4 MG I 1 1203 2002 MG MO6 . BA 5 NAG J 1 401 401 NAG NAG . CA 5 NAG J 1 402 402 NAG NAG . DA 6 AH2 J 1 403 403 AH2 MAN . EA 5 NAG J 1 404 404 NAG NAG . FA 5 NAG J 1 405 405 NAG NAG . GA 3 P5S M 1 1201 1999 P5S P5S . HA 4 MG M 1 1202 2002 MG MO6 . IA 5 NAG N 1 401 401 NAG NAG . JA 5 NAG N 1 402 402 NAG NAG . KA 6 AH2 N 1 403 403 AH2 MAN . LA 5 NAG N 1 404 404 NAG NAG . MA 5 NAG N 1 405 405 NAG NAG . NA 7 HOH A 1 1301 2002 HOH MO6 . NA 7 HOH A 2 1302 2002 HOH MO6 . OA 7 HOH E 1 1301 2002 HOH MO6 . OA 7 HOH E 2 1302 2002 HOH MO6 . PA 7 HOH I 1 1301 2002 HOH MO6 . PA 7 HOH I 2 1302 2002 HOH MO6 . QA 7 HOH M 1 1301 2002 HOH MO6 . QA 7 HOH M 2 1302 2002 HOH MO6 . # 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 O3 AH2 . . . V 6 -35.219 89.538 -6.208 1 165.7 ? O3 AH2 403 F 1 HETATM 2 C C4 AH2 . . . V 6 -36.715 88.59 -7.912 1 165.87 ? C4 AH2 403 F 1 HETATM 3 C C5 AH2 . . . V 6 -36.772 87.752 -9.229 1 161.81 ? C5 AH2 403 F 1 HETATM 4 O O4 AH2 . . . V 6 -37.466 87.928 -6.895 1 166.19 ? O4 AH2 403 F 1 HETATM 5 C C6 AH2 . . . V 6 -37.982 88.068 -10.09 1 149.76 ? C6 AH2 403 F 1 HETATM 6 O O5 AH2 . . . V 6 -35.596 87.972 -10.047 1 168.97 ? O5 AH2 403 F 1 HETATM 7 O O6 AH2 . . . V 6 -39.13 87.604 -9.402 1 143.32 ? O6 AH2 403 F 1 HETATM 8 C C3 AH2 . . . V 6 -35.254 88.806 -7.439 1 165.38 ? C3 AH2 403 F 1 HETATM 9 C C2 AH2 . . . V 6 -34.403 89.492 -8.511 1 165.32 ? C2 AH2 403 F 1 HETATM 10 O O2 AH2 . . . V 6 -34.36 90.891 -8.159 1 161.63 ? O2 AH2 403 F 1 HETATM 11 C C1 AH2 . . . V 6 -34.991 89.241 -9.926 1 170.25 ? C1 AH2 403 F 1 # _model_server_stats.io_time_ms 103 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 72 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 11 #