data_5F5Q # _model_server_result.job_id NDMAQR1mG8szdbS6LNlptw _model_server_result.datetime_utc '2025-01-10 07:32:45' _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 5f5q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":303}' # _entry.id 5F5Q # _exptl.entry_id 5F5Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 194.182 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'methyl alpha-D-mannopyranoside' _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 5F5Q _cell.length_a 60.25 _cell.length_b 81.74 _cell.length_c 86.93 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F5Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 2 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 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 OE1 GLU 8 A GLU 8 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc2 A OD1 ASP 10 A ASP 10 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc3 A OD2 ASP 10 A ASP 10 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc4 A OD2 ASP 10 A ASP 10 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc5 A O TYR 12 A TYR 12 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc6 A OD1 ASN 14 A ASN 14 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc7 A OD2 ASP 19 A ASP 19 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc8 A OD1 ASP 19 A ASP 19 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc9 A NE2 HIS 24 A HIS 24 1_555 D MN MN . A MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc10 C CA CA . A CA 301 1_555 I O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc11 C CA CA . A CA 301 1_555 I O HOH . A HOH 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc12 D MN MN . A MN 302 1_555 I O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc13 D MN MN . A MN 302 1_555 I O HOH . A HOH 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? metalc ? metalc14 B OE1 GLU 8 B GLU 8 1_555 G MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc15 B OD1 ASP 10 B ASP 10 1_555 F CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc16 B OD2 ASP 10 B ASP 10 1_555 F CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.1 ? metalc ? metalc17 B OD2 ASP 10 B ASP 10 1_555 G MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.828 ? metalc ? metalc18 B O TYR 12 B TYR 12 1_555 F CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc19 B OD1 ASN 14 B ASN 14 1_555 F CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc20 B OD2 ASP 19 B ASP 19 1_555 F CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.684 ? metalc ? metalc21 B OD2 ASP 19 B ASP 19 1_555 G MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc22 B NE2 HIS 24 B HIS 24 1_555 G MN MN . B MN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc23 F CA CA . B CA 301 1_555 J O HOH . B HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc24 F CA CA . B CA 301 1_555 J O HOH . B HOH 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc25 G MN MN . B MN 302 1_555 J O HOH . B HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc26 G MN MN . B MN 302 1_555 J O HOH . B HOH 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? # _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 5F5Q _atom_sites.fract_transf_matrix[1][1] 0.016598 _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] 0.012234 _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] 0.011504 _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 CA A 1 301 238 CA CA . D 3 MN A 1 302 239 MN MN . E 4 MMA A 1 303 240 MMA MMA . F 2 CA B 1 301 238 CA CA . G 3 MN B 1 302 239 MN MN . H 4 MMA B 1 303 240 MMA MMA . I 5 HOH A 1 401 56 HOH HOH . I 5 HOH A 2 402 81 HOH HOH . I 5 HOH A 3 403 2 HOH HOH . I 5 HOH A 4 404 93 HOH HOH . I 5 HOH A 5 405 72 HOH HOH . I 5 HOH A 6 406 95 HOH HOH . I 5 HOH A 7 407 16 HOH HOH . I 5 HOH A 8 408 21 HOH HOH . I 5 HOH A 9 409 91 HOH HOH . I 5 HOH A 10 410 36 HOH HOH . I 5 HOH A 11 411 7 HOH HOH . I 5 HOH A 12 412 32 HOH HOH . I 5 HOH A 13 413 54 HOH HOH . I 5 HOH A 14 414 62 HOH HOH . I 5 HOH A 15 415 22 HOH HOH . I 5 HOH A 16 416 80 HOH HOH . I 5 HOH A 17 417 82 HOH HOH . I 5 HOH A 18 418 76 HOH HOH . I 5 HOH A 19 419 17 HOH HOH . I 5 HOH A 20 420 75 HOH HOH . I 5 HOH A 21 421 52 HOH HOH . I 5 HOH A 22 422 65 HOH HOH . I 5 HOH A 23 423 23 HOH HOH . I 5 HOH A 24 424 4 HOH HOH . I 5 HOH A 25 425 41 HOH HOH . I 5 HOH A 26 426 1 HOH HOH . I 5 HOH A 27 427 15 HOH HOH . I 5 HOH A 28 428 63 HOH HOH . I 5 HOH A 29 429 59 HOH HOH . I 5 HOH A 30 430 11 HOH HOH . I 5 HOH A 31 431 97 HOH HOH . I 5 HOH A 32 432 94 HOH HOH . I 5 HOH A 33 433 98 HOH HOH . I 5 HOH A 34 434 38 HOH HOH . I 5 HOH A 35 435 50 HOH HOH . I 5 HOH A 36 436 42 HOH HOH . I 5 HOH A 37 437 57 HOH HOH . I 5 HOH A 38 438 18 HOH HOH . I 5 HOH A 39 439 40 HOH HOH . I 5 HOH A 40 440 87 HOH HOH . I 5 HOH A 41 441 73 HOH HOH . I 5 HOH A 42 442 48 HOH HOH . I 5 HOH A 43 443 6 HOH HOH . I 5 HOH A 44 444 55 HOH HOH . I 5 HOH A 45 445 71 HOH HOH . I 5 HOH A 46 446 46 HOH HOH . I 5 HOH A 47 447 3 HOH HOH . I 5 HOH A 48 448 84 HOH HOH . I 5 HOH A 49 449 53 HOH HOH . I 5 HOH A 50 450 29 HOH HOH . I 5 HOH A 51 451 85 HOH HOH . I 5 HOH A 52 452 58 HOH HOH . I 5 HOH A 53 453 26 HOH HOH . I 5 HOH A 54 454 10 HOH HOH . I 5 HOH A 55 455 27 HOH HOH . I 5 HOH A 56 456 78 HOH HOH . I 5 HOH A 57 457 20 HOH HOH . I 5 HOH A 58 458 83 HOH HOH . I 5 HOH A 59 459 61 HOH HOH . I 5 HOH A 60 460 45 HOH HOH . I 5 HOH A 61 461 33 HOH HOH . I 5 HOH A 62 462 34 HOH HOH . I 5 HOH A 63 463 88 HOH HOH . I 5 HOH A 64 464 68 HOH HOH . I 5 HOH A 65 465 69 HOH HOH . I 5 HOH A 66 466 70 HOH HOH . I 5 HOH A 67 467 92 HOH HOH . J 5 HOH B 1 401 77 HOH HOH . J 5 HOH B 2 402 66 HOH HOH . J 5 HOH B 3 403 86 HOH HOH . J 5 HOH B 4 404 19 HOH HOH . J 5 HOH B 5 405 74 HOH HOH . J 5 HOH B 6 406 8 HOH HOH . J 5 HOH B 7 407 14 HOH HOH . J 5 HOH B 8 408 12 HOH HOH . J 5 HOH B 9 409 49 HOH HOH . J 5 HOH B 10 410 39 HOH HOH . J 5 HOH B 11 411 5 HOH HOH . J 5 HOH B 12 412 31 HOH HOH . J 5 HOH B 13 413 43 HOH HOH . J 5 HOH B 14 414 35 HOH HOH . J 5 HOH B 15 415 60 HOH HOH . J 5 HOH B 16 416 13 HOH HOH . J 5 HOH B 17 417 9 HOH HOH . J 5 HOH B 18 418 67 HOH HOH . J 5 HOH B 19 419 51 HOH HOH . J 5 HOH B 20 420 25 HOH HOH . J 5 HOH B 21 421 64 HOH HOH . J 5 HOH B 22 422 96 HOH HOH . J 5 HOH B 23 423 79 HOH HOH . J 5 HOH B 24 424 44 HOH HOH . J 5 HOH B 25 425 89 HOH HOH . J 5 HOH B 26 426 47 HOH HOH . J 5 HOH B 27 427 90 HOH HOH . J 5 HOH B 28 428 24 HOH HOH . J 5 HOH B 29 429 30 HOH HOH . J 5 HOH B 30 430 28 HOH HOH . J 5 HOH B 31 431 37 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 . . . H 4 27.446 -44.464 -22.775 1 34.23 ? C1 MMA 303 B 1 HETATM 2 C C2 MMA . . . H 4 27.714 -44.505 -21.276 1 33.35 ? C2 MMA 303 B 1 HETATM 3 C C3 MMA . . . H 4 26.455 -44.889 -20.507 1 33.96 ? C3 MMA 303 B 1 HETATM 4 C C4 MMA . . . H 4 25.265 -44.049 -20.952 1 34.53 ? C4 MMA 303 B 1 HETATM 5 C C5 MMA . . . H 4 25.143 -44.035 -22.471 1 33.71 ? C5 MMA 303 B 1 HETATM 6 C C6 MMA . . . H 4 23.999 -43.134 -22.919 1 32.07 ? C6 MMA 303 B 1 HETATM 7 C C7 MMA . . . H 4 28.105 -46.304 -24.101 1 39.4 ? C7 MMA 303 B 1 HETATM 8 O O1 MMA . . . H 4 27.106 -45.771 -23.234 1 35.2 ? O1 MMA 303 B 1 HETATM 9 O O2 MMA . . . H 4 28.168 -43.22 -20.836 1 30.29 ? O2 MMA 303 B 1 HETATM 10 O O3 MMA . . . H 4 26.676 -44.699 -19.105 1 32.79 ? O3 MMA 303 B 1 HETATM 11 O O4 MMA . . . H 4 24.064 -44.582 -20.382 1 33.9 ? O4 MMA 303 B 1 HETATM 12 O O5 MMA . . . H 4 26.365 -43.571 -23.041 1 35.59 ? O5 MMA 303 B 1 HETATM 13 O O6 MMA . . . H 4 24.491 -41.805 -23.125 1 31.46 ? O6 MMA 303 B 1 # _model_server_stats.io_time_ms 80 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #