data_4GKY # _model_server_result.job_id HIDszMWfCMFvFiTGggOvYw _model_server_result.datetime_utc '2024-10-28 02:29:57' _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 4gky # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":303}' # _entry.id 4GKY # _exptl.entry_id 4GKY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 180.156 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description alpha-D-mannopyranose _entity.pdbx_number_of_molecules 1 _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 120 _cell.entry_id 4GKY _cell.length_a 110.263 _cell.length_b 110.263 _cell.length_c 38.332 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GKY _symmetry.cell_setting ? _symmetry.Int_Tables_number 168 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 6' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A SG CYS 181 A CYS 190 1_555 A SG CYS 221 A CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc1 A OD2 ASP 143 A ASP 152 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc2 A OD1 ASP 143 A ASP 152 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc3 A O PHE 145 A PHE 154 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc4 A OD1 ASP 146 A ASP 155 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc5 A OD1 ASN 147 A ASN 156 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc6 A OD1 ASP 148 A ASP 157 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc7 A OD2 ASP 148 A ASP 157 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.873 ? metalc ? metalc8 A OD1 ASN 152 A ASN 161 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc9 A OD1 ASN 153 A ASN 162 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc10 A OD1 ASP 172 A ASP 181 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc11 A OD2 ASP 172 A ASP 181 1_555 C CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.402 ? metalc ? metalc12 B CA CA . A CA 301 1_555 G O HOH . A HOH 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.597 ? metalc ? metalc13 B CA CA . A CA 301 1_555 G O HOH . A HOH 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc14 C CA CA . A CA 302 1_555 G O HOH . A HOH 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.661 ? # _chem_comp.formula 'C6 H12 O6' _chem_comp.formula_weight 180.156 _chem_comp.id MAN _chem_comp.mon_nstd_flag . _chem_comp.name alpha-D-mannopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms alpha-D-mannose;D-mannose;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 C2 MAN sing 231 n n C1 O1 MAN sing 232 n n C1 O5 MAN sing 233 n n C1 H1 MAN sing 234 n n C2 C3 MAN sing 235 n n C2 O2 MAN sing 236 n n C2 H2 MAN sing 237 n n C3 C4 MAN sing 238 n n C3 O3 MAN sing 239 n n C3 H3 MAN sing 240 n n C4 C5 MAN sing 241 n n C4 O4 MAN sing 242 n n C4 H4 MAN sing 243 n n C5 C6 MAN sing 244 n n C5 O5 MAN sing 245 n n C5 H5 MAN sing 246 n n C6 O6 MAN sing 247 n n C6 H61 MAN sing 248 n n C6 H62 MAN sing 249 n n O1 HO1 MAN sing 250 n n O2 HO2 MAN sing 251 n n O3 HO3 MAN sing 252 n n O4 HO4 MAN sing 253 n n O6 HO6 MAN sing 254 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 MAN DManpa 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 MAN a-D-mannopyranose 'COMMON NAME' GMML 1 MAN a-D-Manp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 MAN Man 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4GKY _atom_sites.fract_transf_matrix[1][1] 0.009069 _atom_sites.fract_transf_matrix[1][2] 0.005236 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010472 _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] 0.026088 _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 B 2 CA A 1 301 500 CA CA . C 2 CA A 1 302 501 CA CA . D 3 MAN A 1 303 600 MAN MAN . E 4 GOL A 1 304 1 GOL GOL . F 4 GOL A 1 305 2 GOL GOL . G 5 HOH A 1 401 1 HOH HOH . G 5 HOH A 2 402 3 HOH HOH . G 5 HOH A 3 403 4 HOH HOH . G 5 HOH A 4 404 5 HOH HOH . G 5 HOH A 5 405 7 HOH HOH . G 5 HOH A 6 406 10 HOH HOH . G 5 HOH A 7 407 11 HOH HOH . G 5 HOH A 8 408 12 HOH HOH . G 5 HOH A 9 409 13 HOH HOH . G 5 HOH A 10 410 14 HOH HOH . G 5 HOH A 11 411 15 HOH HOH . G 5 HOH A 12 412 18 HOH HOH . G 5 HOH A 13 413 19 HOH HOH . G 5 HOH A 14 414 20 HOH HOH . G 5 HOH A 15 415 21 HOH HOH . G 5 HOH A 16 416 22 HOH HOH . G 5 HOH A 17 417 23 HOH HOH . G 5 HOH A 18 418 24 HOH HOH . G 5 HOH A 19 419 25 HOH HOH . G 5 HOH A 20 420 26 HOH HOH . G 5 HOH A 21 421 27 HOH HOH . G 5 HOH A 22 422 28 HOH HOH . G 5 HOH A 23 423 30 HOH HOH . G 5 HOH A 24 424 31 HOH HOH . G 5 HOH A 25 425 32 HOH HOH . G 5 HOH A 26 426 36 HOH HOH . G 5 HOH A 27 427 37 HOH HOH . G 5 HOH A 28 428 38 HOH HOH . G 5 HOH A 29 429 39 HOH HOH . G 5 HOH A 30 430 40 HOH HOH . G 5 HOH A 31 431 41 HOH HOH . G 5 HOH A 32 432 42 HOH HOH . G 5 HOH A 33 433 43 HOH HOH . G 5 HOH A 34 434 44 HOH HOH . G 5 HOH A 35 435 45 HOH HOH . G 5 HOH A 36 436 46 HOH HOH . G 5 HOH A 37 437 54 HOH HOH . G 5 HOH A 38 438 55 HOH HOH . G 5 HOH A 39 439 56 HOH HOH . G 5 HOH A 40 440 57 HOH HOH . G 5 HOH A 41 441 60 HOH HOH . G 5 HOH A 42 442 61 HOH HOH . G 5 HOH A 43 443 62 HOH HOH . G 5 HOH A 44 444 63 HOH HOH . G 5 HOH A 45 445 64 HOH HOH . G 5 HOH A 46 446 65 HOH HOH . G 5 HOH A 47 447 69 HOH HOH . G 5 HOH A 48 448 70 HOH HOH . G 5 HOH A 49 449 71 HOH HOH . G 5 HOH A 50 450 72 HOH HOH . G 5 HOH A 51 451 73 HOH HOH . G 5 HOH A 52 452 74 HOH HOH . G 5 HOH A 53 453 75 HOH HOH . G 5 HOH A 54 454 77 HOH HOH . G 5 HOH A 55 455 78 HOH HOH . G 5 HOH A 56 456 79 HOH HOH . G 5 HOH A 57 457 80 HOH HOH . G 5 HOH A 58 458 81 HOH HOH . G 5 HOH A 59 459 90 HOH HOH . G 5 HOH A 60 460 93 HOH HOH . G 5 HOH A 61 461 94 HOH HOH . G 5 HOH A 62 462 96 HOH HOH . G 5 HOH A 63 463 97 HOH HOH . G 5 HOH A 64 464 98 HOH HOH . G 5 HOH A 65 465 99 HOH HOH . G 5 HOH A 66 466 100 HOH HOH . G 5 HOH A 67 467 101 HOH HOH . G 5 HOH A 68 468 102 HOH HOH . G 5 HOH A 69 469 104 HOH HOH . G 5 HOH A 70 470 105 HOH HOH . G 5 HOH A 71 471 107 HOH HOH . G 5 HOH A 72 472 108 HOH HOH . G 5 HOH A 73 473 109 HOH HOH . G 5 HOH A 74 474 110 HOH HOH . G 5 HOH A 75 475 111 HOH HOH . G 5 HOH A 76 476 112 HOH HOH . G 5 HOH A 77 477 113 HOH HOH . G 5 HOH A 78 478 114 HOH HOH . G 5 HOH A 79 479 115 HOH HOH . G 5 HOH A 80 480 116 HOH HOH . G 5 HOH A 81 481 118 HOH HOH . G 5 HOH A 82 482 119 HOH HOH . G 5 HOH A 83 483 120 HOH HOH . G 5 HOH A 84 484 121 HOH HOH . G 5 HOH A 85 485 122 HOH HOH . G 5 HOH A 86 486 124 HOH HOH . G 5 HOH A 87 487 126 HOH HOH . G 5 HOH A 88 488 127 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 MAN . . . D 3 12.134 132.386 8.918 0.9 54.89 ? C1 MAN 303 A 1 HETATM 2 C C2 MAN . . . D 3 11.241 132.777 10.082 0.9 56.17 ? C2 MAN 303 A 1 HETATM 3 C C3 MAN . . . D 3 10.318 133.923 9.679 0.9 58.75 ? C3 MAN 303 A 1 HETATM 4 C C4 MAN . . . D 3 11.087 135.034 9.003 0.9 52.59 ? C4 MAN 303 A 1 HETATM 5 C C5 MAN . . . D 3 11.811 134.432 7.832 0.9 57.64 ? C5 MAN 303 A 1 HETATM 6 C C6 MAN . . . D 3 12.604 135.496 7.114 0.9 57.96 ? C6 MAN 303 A 1 HETATM 7 O O1 MAN . . . D 3 11.406 131.759 7.898 0.9 61.36 ? O1 MAN 303 A 1 HETATM 8 O O2 MAN . . . D 3 12.012 133.118 11.222 0.9 58.79 ? O2 MAN 303 A 1 HETATM 9 O O3 MAN . . . D 3 9.716 134.432 10.847 0.9 63.38 ? O3 MAN 303 A 1 HETATM 10 O O4 MAN . . . D 3 10.202 136.008 8.556 0.9 57.1 ? O4 MAN 303 A 1 HETATM 11 O O5 MAN . . . D 3 12.733 133.496 8.322 0.9 61.81 ? O5 MAN 303 A 1 HETATM 12 O O6 MAN . . . D 3 13.678 135.918 7.934 0.9 56.03 ? O6 MAN 303 A 1 HETATM 13 H H1 MAN . . . D 3 12.909 131.707 9.273 0.9 65.86 ? H1 MAN 303 A 1 HETATM 14 H H2 MAN . . . D 3 10.622 131.918 10.338 0.9 67.4 ? H2 MAN 303 A 1 HETATM 15 H H3 MAN . . . D 3 9.547 133.55 9.005 0.9 70.5 ? H3 MAN 303 A 1 HETATM 16 H H4 MAN . . . D 3 11.802 135.471 9.701 0.9 63.11 ? H4 MAN 303 A 1 HETATM 17 H H5 MAN . . . D 3 11.107 133.955 7.15 0.9 69.17 ? H5 MAN 303 A 1 HETATM 18 H H61 MAN . . . D 3 11.957 136.346 6.897 0.9 69.55 ? H61 MAN 303 A 1 HETATM 19 H H62 MAN . . . D 3 12.995 135.091 6.182 0.9 69.55 ? H62 MAN 303 A 1 HETATM 20 H HO1 MAN . . . D 3 11.983 131.084 7.517 0.9 73.63 ? HO1 MAN 303 A 1 HETATM 21 H HO2 MAN . . . D 3 11.941 132.377 11.839 0.9 70.55 ? HO2 MAN 303 A 1 HETATM 22 H HO3 MAN . . . D 3 9.342 133.676 11.321 0.9 76.06 ? HO3 MAN 303 A 1 HETATM 23 H HO4 MAN . . . D 3 10.666 136.854 8.609 0.9 68.52 ? HO4 MAN 303 A 1 HETATM 24 H HO6 MAN . . . D 3 14.481 135.857 7.398 0.9 67.24 ? HO6 MAN 303 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 24 #