data_3OJY # _model_server_result.job_id jpT5pWz4YHeHZemyODkprA _model_server_result.datetime_utc '2024-12-21 11:34:08' _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 3ojy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":556}' # _entry.id 3OJY # _exptl.entry_id 3OJY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 180.156 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-mannopyranose _entity.pdbx_number_of_molecules 8 _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 3OJY _cell.length_a 139.575 _cell.length_b 139.575 _cell.length_c 127.16 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OJY _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,K,L,M _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 E N N ? 5 F N N ? 5 G N N ? 5 H N N ? 5 J N N ? 5 K N N ? 5 L N N ? 5 M 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 A SG CYS 9 A CYS 9 1_555 A SG CYS 44 A CYS 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf2 A SG CYS 20 A CYS 20 1_555 A SG CYS 54 A CYS 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf3 A SG CYS 23 A CYS 23 1_555 A SG CYS 60 A CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf4 A SG CYS 66 A CYS 66 1_555 A SG CYS 78 A CYS 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 72 A CYS 72 1_555 A SG CYS 91 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf6 A SG CYS 85 A CYS 85 1_555 A SG CYS 100 A CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 110 A CYS 110 1_555 A SG CYS 147 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 A SG CYS 164 A CYS 164 1_555 C SG CYS 40 C CYS 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf9 A SG CYS 467 A CYS 467 1_555 A SG CYS 514 A CYS 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf10 A SG CYS 469 A CYS 469 1_555 A SG CYS 485 A CYS 485 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf11 A SG CYS 472 A CYS 472 1_555 A SG CYS 487 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? disulf ? disulf12 A SG CYS 489 A CYS 489 1_555 A SG CYS 498 A CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf13 A SG CYS 532 A CYS 532 1_555 A SG CYS 544 A CYS 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf14 B SG CYS 11 B CYS 11 1_555 B SG CYS 46 B CYS 46 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf15 B SG CYS 22 B CYS 22 1_555 B SG CYS 56 B CYS 56 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf16 B SG CYS 25 B CYS 25 1_555 B SG CYS 62 B CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf17 B SG CYS 68 B CYS 68 1_555 B SG CYS 79 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf18 B SG CYS 73 B CYS 73 1_555 B SG CYS 92 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf19 B SG CYS 86 B CYS 86 1_555 B SG CYS 101 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf20 B SG CYS 324 B CYS 324 1_555 B SG CYS 349 B CYS 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? disulf ? disulf21 B SG CYS 449 B CYS 449 1_555 B SG CYS 496 B CYS 496 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf22 B SG CYS 451 B CYS 451 1_555 B SG CYS 467 B CYS 467 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf23 B SG CYS 454 B CYS 454 1_555 B SG CYS 469 B CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? disulf ? disulf24 B SG CYS 471 B CYS 471 1_555 B SG CYS 480 B CYS 480 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? disulf ? disulf25 B SG CYS 503 B CYS 503 1_555 B SG CYS 536 B CYS 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf26 C SG CYS 76 C CYS 76 1_555 C SG CYS 168 C CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? covale ? covale1 A CD1 TRP 14 A TRP 14 1_555 E C1 BMA . A BMA 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale2 A CD1 TRP 512 A TRP 512 1_555 F C1 BMA . A BMA 557 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale3 A CD1 TRP 515 A TRP 515 1_555 G C1 BMA . A BMA 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? covale ? covale4 A CD1 TRP 518 A TRP 518 1_555 H C1 BMA . A BMA 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.5 ? covale ? covale5 B CD1 TRP 16 B TRP 16 1_555 J C1 BMA . B BMA 539 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale6 B CD1 TRP 19 B TRP 19 1_555 K C1 BMA . B BMA 540 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale7 B C ASP 363 B ASP 363 1_555 B N TPO 364 B TPO 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale8 B C TPO 364 B TPO 364 1_555 B N MET 365 B MET 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale9 B CD1 TRP 497 B TRP 497 1_555 L C1 BMA . B BMA 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.5 ? covale ? covale10 B CD1 TRP 500 B TRP 500 1_555 M C1 BMA . B BMA 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.475 ? metalc ? metalc1 A O LEU 83 A LEU 83 1_555 D CA CA . A CA 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc2 A OD1 ASN 86 A ASN 86 1_555 D CA CA . A CA 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc3 A O ASP 88 A ASP 88 1_555 D CA CA . A CA 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc4 A OD1 ASP 90 A ASP 90 1_555 D CA CA . A CA 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc5 A OD1 ASP 96 A ASP 96 1_555 D CA CA . A CA 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc6 A OE2 GLU 97 A GLU 97 1_555 D CA CA . A CA 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc7 B O LEU 84 B LEU 84 1_555 I CA CA . B CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc8 B OD1 ASN 87 B ASN 87 1_555 I CA CA . B CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc9 B O ASP 89 B ASP 89 1_555 I CA CA . B CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc10 B OD2 ASP 91 B ASP 91 1_555 I CA CA . B CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc11 B OD1 ASP 97 B ASP 97 1_555 I CA CA . B CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc12 B OE2 GLU 98 B GLU 98 1_555 I CA CA . B CA 538 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? # _chem_comp.formula 'C6 H12 O6' _chem_comp.formula_weight 180.156 _chem_comp.id BMA _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-mannopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-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 BMA sing 70 n n C1 O1 BMA sing 71 n n C1 O5 BMA sing 72 n n C1 H1 BMA sing 73 n n C2 C3 BMA sing 74 n n C2 O2 BMA sing 75 n n C2 H2 BMA sing 76 n n C3 C4 BMA sing 77 n n C3 O3 BMA sing 78 n n C3 H3 BMA sing 79 n n C4 C5 BMA sing 80 n n C4 O4 BMA sing 81 n n C4 H4 BMA sing 82 n n C5 C6 BMA sing 83 n n C5 O5 BMA sing 84 n n C5 H5 BMA sing 85 n n C6 O6 BMA sing 86 n n C6 H61 BMA sing 87 n n C6 H62 BMA sing 88 n n O1 HO1 BMA sing 89 n n O2 HO2 BMA sing 90 n n O3 HO3 BMA sing 91 n n O4 HO4 BMA sing 92 n n O6 HO6 BMA sing 93 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 BMA DManpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 BMA b-D-mannopyranose 'COMMON NAME' GMML 1 BMA b-D-Manp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 BMA Man 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3OJY _atom_sites.fract_transf_matrix[1][1] 0.007165 _atom_sites.fract_transf_matrix[1][2] 0.004136 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008273 _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] 0.007864 _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 D 4 CA A 1 555 1 CA CA . E 5 BMA A 1 556 14 BMA BMA . F 5 BMA A 1 557 512 BMA BMA . G 5 BMA A 1 558 515 BMA BMA . H 5 BMA A 1 559 518 BMA BMA . I 4 CA B 1 538 2 CA CA . J 5 BMA B 1 539 16 BMA BMA . K 5 BMA B 1 540 19 BMA BMA . L 5 BMA B 1 541 497 BMA BMA . M 5 BMA B 1 542 500 BMA BMA . # 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 BMA . . . E 5 23.804 -43.38 -20.292 1 47.51 ? C1 BMA 556 A 1 HETATM 2 C C2 BMA . . . E 5 24.895 -44.244 -20.976 1 49.42 ? C2 BMA 556 A 1 HETATM 3 C C3 BMA . . . E 5 24.441 -45.686 -21.083 1 51.18 ? C3 BMA 556 A 1 HETATM 4 C C4 BMA . . . E 5 22.93 -45.707 -21.249 1 52.63 ? C4 BMA 556 A 1 HETATM 5 C C5 BMA . . . E 5 22.195 -45.064 -20.061 1 54.04 ? C5 BMA 556 A 1 HETATM 6 C C6 BMA . . . E 5 21.721 -46.156 -19.106 1 56.44 ? C6 BMA 556 A 1 HETATM 7 O O2 BMA . . . E 5 26.153 -44.27 -20.296 1 48.85 ? O2 BMA 556 A 1 HETATM 8 O O3 BMA . . . E 5 24.844 -46.378 -19.893 1 50.61 ? O3 BMA 556 A 1 HETATM 9 O O4 BMA . . . E 5 22.662 -44.971 -22.451 1 53.54 ? O4 BMA 556 A 1 HETATM 10 O O5 BMA . . . E 5 23.016 -44.097 -19.359 1 52.17 ? O5 BMA 556 A 1 HETATM 11 O O6 BMA . . . E 5 22.763 -46.454 -18.153 1 59.31 ? O6 BMA 556 A 1 # _model_server_stats.io_time_ms 76 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 11 #