data_3D87 # _model_server_result.job_id JW1TWykHj-NrcRitiJrZwg _model_server_result.datetime_utc '2024-11-22 13:01:19' _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 3d87 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1281}' # _entry.id 3D87 # _exptl.entry_id 3D87 _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 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 90 _cell.entry_id 3D87 _cell.length_a 110.098 _cell.length_b 240.587 _cell.length_c 141.781 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3D87 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 tetrameric 4 software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 1 A,B,E,F 2 1 C,D,G,H,I 3 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 5 _struct_asym.id G _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 metalc ? metalc1 B O LEU 95 B LEU 95 1_555 F K K . B K 5004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc2 D O THR 92 D THR 92 1_555 I K K . D K 5003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc3 D O LEU 95 D LEU 95 1_555 I K K . D K 5003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? # _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 216 n n C1 O1 MAN sing 217 n n C1 O5 MAN sing 218 n n C1 H1 MAN sing 219 n n C2 C3 MAN sing 220 n n C2 O2 MAN sing 221 n n C2 H2 MAN sing 222 n n C3 C4 MAN sing 223 n n C3 O3 MAN sing 224 n n C3 H3 MAN sing 225 n n C4 C5 MAN sing 226 n n C4 O4 MAN sing 227 n n C4 H4 MAN sing 228 n n C5 C6 MAN sing 229 n n C5 O5 MAN sing 230 n n C5 H5 MAN sing 231 n n C6 O6 MAN sing 232 n n C6 H61 MAN sing 233 n n C6 H62 MAN sing 234 n n O1 HO1 MAN sing 235 n n O2 HO2 MAN sing 236 n n O3 HO3 MAN sing 237 n n O4 HO4 MAN sing 238 n n O6 HO6 MAN sing 239 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 3D87 _atom_sites.fract_transf_matrix[1][1] 0.009083 _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] 0.004157 _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] 0.007053 _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 3 PO4 B 1 5001 5001 PO4 PO4 . F 4 K B 1 5004 5004 K K . G 5 MAN D 1 1281 1281 MAN MAN . H 3 PO4 D 1 5002 5002 PO4 PO4 . I 4 K D 1 5003 5003 K K . # 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 . . . G 5 4.708 17.387 40.854 1 128.48 ? C1 MAN 1281 D 1 HETATM 2 C C2 MAN . . . G 5 4.989 15.896 41.228 1 130.42 ? C2 MAN 1281 D 1 HETATM 3 C C3 MAN . . . G 5 6.027 15.225 40.257 1 131.08 ? C3 MAN 1281 D 1 HETATM 4 C C4 MAN . . . G 5 6.101 15.796 38.773 1 130.97 ? C4 MAN 1281 D 1 HETATM 5 C C5 MAN . . . G 5 5.621 17.287 38.623 1 130.84 ? C5 MAN 1281 D 1 HETATM 6 C C6 MAN . . . G 5 5.476 17.773 37.134 1 132 ? C6 MAN 1281 D 1 HETATM 7 O O2 MAN . . . G 5 3.778 15.106 41.47 1 131.88 ? O2 MAN 1281 D 1 HETATM 8 O O3 MAN . . . G 5 5.945 13.777 40.304 1 133.05 ? O3 MAN 1281 D 1 HETATM 9 O O4 MAN . . . G 5 7.404 15.584 38.165 1 132.16 ? O4 MAN 1281 D 1 HETATM 10 O O5 MAN . . . G 5 4.446 17.584 39.444 1 129.67 ? O5 MAN 1281 D 1 HETATM 11 O O6 MAN . . . G 5 4.669 18.98 36.944 1 133.62 ? O6 MAN 1281 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 11 #