data_7MGC # _model_server_result.job_id jMt8w-ePzl_0f_N6ocm7Mg _model_server_result.datetime_utc '2024-11-01 19:41:01' _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 7mgc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":301}' # _entry.id 7MGC # _exptl.entry_id 7MGC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 194.182 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'methyl alpha-D-mannopyranoside' _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 7MGC _cell.length_a 69.33 _cell.length_b 117.34 _cell.length_c 122.4 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7MGC _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,K,L,M,Q,S 1 1 B,D,H,I,J,N,O,P,R,T 1 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_545 -x,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 -58.67 61.2 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 E N N ? 2 H N N ? 2 K N N ? 2 N 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 OE2 GLU 8 A GLU 8 1_555 F MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc2 A OD2 ASP 10 A ASP 10 1_555 F MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc3 A OD1 ASP 10 A ASP 10 1_555 G CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc4 A OD2 ASP 10 A ASP 10 1_555 G CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? metalc ? metalc5 A O TYR 12 A TYR 12 1_555 G CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc6 A OD1 ASN 14 A ASN 14 1_555 G CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc7 A OD1 ASP 19 A ASP 19 1_555 F MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc8 A OD2 ASP 19 A ASP 19 1_555 G CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc9 A NE2 HIS 24 A HIS 24 1_555 F MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc10 F MN MN . A MN 302 1_555 Q O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc11 B OE2 GLU 8 B GLU 8 1_555 I MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc12 B OD2 ASP 10 B ASP 10 1_555 I MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc13 B OD1 ASP 10 B ASP 10 1_555 J CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc14 B OD2 ASP 10 B ASP 10 1_555 J CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? metalc ? metalc15 B O TYR 12 B TYR 12 1_555 J CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc16 B OD1 ASN 14 B ASN 14 1_555 J CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc17 B OD1 ASP 19 B ASP 19 1_555 I MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.785 ? metalc ? metalc18 B OD2 ASP 19 B ASP 19 1_555 J CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc19 B NE2 HIS 24 B HIS 24 1_555 I MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc20 C OE2 GLU 8 C GLU 8 1_555 L MN MN . C MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.859 ? metalc ? metalc21 C OD2 ASP 10 C ASP 10 1_555 L MN MN . C MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? metalc ? metalc22 C OD1 ASP 10 C ASP 10 1_555 M CA CA . C CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc23 C OD2 ASP 10 C ASP 10 1_555 M CA CA . C CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.612 ? metalc ? metalc24 C O TYR 12 C TYR 12 1_555 M CA CA . C CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc25 C OD1 ASN 14 C ASN 14 1_555 M CA CA . C CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc26 C OD1 ASP 19 C ASP 19 1_555 L MN MN . C MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc27 C OD2 ASP 19 C ASP 19 1_555 M CA CA . C CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc28 C NE2 HIS 24 C HIS 24 1_555 L MN MN . C MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc29 D OE2 GLU 8 D GLU 8 1_555 O MN MN . D MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.749 ? metalc ? metalc30 D OD2 ASP 10 D ASP 10 1_555 O MN MN . D MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc31 D OD1 ASP 10 D ASP 10 1_555 P CA CA . D CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc32 D OD2 ASP 10 D ASP 10 1_555 P CA CA . D CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc33 D O TYR 12 D TYR 12 1_555 P CA CA . D CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc34 D OD1 ASN 14 D ASN 14 1_555 P CA CA . D CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.957 ? metalc ? metalc35 D OD1 ASP 19 D ASP 19 1_555 O MN MN . D MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc36 D OD2 ASP 19 D ASP 19 1_555 P CA CA . D CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc37 D NE2 HIS 24 D HIS 24 1_555 O MN MN . D MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? metalc ? metalc38 O MN MN . D MN 302 1_555 T O HOH . D HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? # _chem_comp.formula 'C7 H14 O6' _chem_comp.formula_weight 194.182 _chem_comp.id MMA _chem_comp.mon_nstd_flag n _chem_comp.name 'methyl alpha-D-mannopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'O1-METHYL-MANNOSE;methyl alpha-D-mannoside;methyl D-mannoside;methyl mannoside' # 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 C2 MMA sing 224 n n C1 O1 MMA sing 225 n n C1 O5 MMA sing 226 n n C1 H1 MMA sing 227 n n C2 C3 MMA sing 228 n n C2 O2 MMA sing 229 n n C2 H2 MMA sing 230 n n C3 C4 MMA sing 231 n n C3 O3 MMA sing 232 n n C3 H3 MMA sing 233 n n C4 C5 MMA sing 234 n n C4 O4 MMA sing 235 n n C4 H4 MMA sing 236 n n C5 C6 MMA sing 237 n n C5 O5 MMA sing 238 n n C5 H5 MMA sing 239 n n C6 O6 MMA sing 240 n n C6 H61 MMA sing 241 n n C6 H62 MMA sing 242 n n C7 O1 MMA sing 243 n n C7 H71 MMA sing 244 n n C7 H72 MMA sing 245 n n C7 H73 MMA sing 246 n n O2 HO2 MMA sing 247 n n O3 HO3 MMA sing 248 n n O4 HO4 MMA sing 249 n n O6 HO6 MMA sing 250 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version MMA DManp[1Me]a 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 MMA 1-methyl-a-D-mannopyranose 'COMMON NAME' GMML 1 MMA o1-methyl-mannose 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 # _atom_sites.entry_id 7MGC _atom_sites.fract_transf_matrix[1][1] 0.014424 _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] 0.008522 _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] 0.00817 _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 E 2 MMA A 1 301 238 MMA MMA . F 3 MN A 1 302 239 MN MN . G 4 CA A 1 303 240 CA CA . H 2 MMA B 1 301 238 MMA MMA . I 3 MN B 1 302 239 MN MN . J 4 CA B 1 303 240 CA CA . K 2 MMA C 1 301 238 MMA MMA . L 3 MN C 1 302 239 MN MN . M 4 CA C 1 303 240 CA CA . N 2 MMA D 1 301 238 MMA MMA . O 3 MN D 1 302 239 MN MN . P 4 CA D 1 303 240 CA CA . Q 5 HOH A 1 401 29 HOH HOH . Q 5 HOH A 2 402 2 HOH HOH . Q 5 HOH A 3 403 39 HOH HOH . Q 5 HOH A 4 404 1 HOH HOH . Q 5 HOH A 5 405 22 HOH HOH . Q 5 HOH A 6 406 34 HOH HOH . Q 5 HOH A 7 407 15 HOH HOH . Q 5 HOH A 8 408 28 HOH HOH . Q 5 HOH A 9 409 11 HOH HOH . Q 5 HOH A 10 410 18 HOH HOH . Q 5 HOH A 11 411 42 HOH HOH . Q 5 HOH A 12 412 44 HOH HOH . Q 5 HOH A 13 413 9 HOH HOH . R 5 HOH B 1 401 21 HOH HOH . R 5 HOH B 2 402 4 HOH HOH . R 5 HOH B 3 403 5 HOH HOH . R 5 HOH B 4 404 8 HOH HOH . R 5 HOH B 5 405 10 HOH HOH . R 5 HOH B 6 406 37 HOH HOH . R 5 HOH B 7 407 19 HOH HOH . S 5 HOH C 1 401 38 HOH HOH . S 5 HOH C 2 402 7 HOH HOH . S 5 HOH C 3 403 24 HOH HOH . S 5 HOH C 4 404 36 HOH HOH . S 5 HOH C 5 405 25 HOH HOH . S 5 HOH C 6 406 26 HOH HOH . S 5 HOH C 7 407 13 HOH HOH . S 5 HOH C 8 408 6 HOH HOH . S 5 HOH C 9 409 27 HOH HOH . T 5 HOH D 1 401 12 HOH HOH . T 5 HOH D 2 402 40 HOH HOH . T 5 HOH D 3 403 16 HOH HOH . T 5 HOH D 4 404 23 HOH HOH . T 5 HOH D 5 405 33 HOH HOH . T 5 HOH D 6 406 14 HOH HOH . T 5 HOH D 7 407 35 HOH HOH . T 5 HOH D 8 408 20 HOH HOH . T 5 HOH D 9 409 3 HOH HOH . T 5 HOH D 10 410 47 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 C C1 MMA . . . K 2 -21.199 17.205 59.602 1 64.1 ? C1 MMA 301 C 1 HETATM 2 C C2 MMA . . . K 2 -19.856 16.674 60.087 1 62.37 ? C2 MMA 301 C 1 HETATM 3 C C3 MMA . . . K 2 -18.814 16.703 58.977 1 66.03 ? C3 MMA 301 C 1 HETATM 4 C C4 MMA . . . K 2 -19.337 16.058 57.699 1 72.68 ? C4 MMA 301 C 1 HETATM 5 C C5 MMA . . . K 2 -20.709 16.614 57.349 1 75.44 ? C5 MMA 301 C 1 HETATM 6 C C6 MMA . . . K 2 -21.31 15.856 56.185 1 77.17 ? C6 MMA 301 C 1 HETATM 7 C C7 MMA . . . K 2 -22.327 19.28 59.609 1 55.11 ? C7 MMA 301 C 1 HETATM 8 O O1 MMA . . . K 2 -21.115 18.596 59.292 1 62.45 ? O1 MMA 301 C 1 HETATM 9 O O2 MMA . . . K 2 -20.018 15.329 60.555 1 59.25 ? O2 MMA 301 C 1 HETATM 10 O O3 MMA . . . K 2 -17.652 16.005 59.432 1 60.32 ? O3 MMA 301 C 1 HETATM 11 O O4 MMA . . . K 2 -18.436 16.325 56.62 1 74.4 ? O4 MMA 301 C 1 HETATM 12 O O5 MMA . . . K 2 -21.598 16.47 58.45 1 69.92 ? O5 MMA 301 C 1 HETATM 13 O O6 MMA . . . K 2 -20.835 14.51 56.216 1 73.87 ? O6 MMA 301 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 13 #