data_2XV7 # _model_server_result.job_id 1o7vzhCuxzG3vBolj_LtDg _model_server_result.datetime_utc '2024-11-22 22:19:39' _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 2xv7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":404}' # _entry.id 2XV7 # _exptl.entry_id 2XV7 _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 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 120 _cell.entry_id 2XV7 _cell.length_a 95.72 _cell.length_b 95.72 _cell.length_c 70.94 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2XV7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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' 10_444 -y-1,-x-1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -47.86 -82.895952 -11.823333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 400 NAG 2 n B NAG 2 B 2 NAG A 401 NAG 2 n B BMA 3 B 3 BMA A 402 BMA 2 n C NAG 1 C 1 NAG A 500 NAG 2 n C NAG 2 C 2 NAG A 501 NAG 2 n C BMA 3 C 3 BMA A 502 BMA # 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 22 A CYS 111 1_555 A SG CYS 64 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 47 A CYS 136 1_555 A SG CYS 56 A CYS 145 10_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 53 A CYS 142 1_555 A SG CYS 100 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 A SG CYS 57 A CYS 146 1_555 A SG CYS 102 A CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 66 A ASN 155 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 A ND2 ASN 96 A ASN 185 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _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 242 n n C1 O1 MAN sing 243 n n C1 O5 MAN sing 244 n n C1 H1 MAN sing 245 n n C2 C3 MAN sing 246 n n C2 O2 MAN sing 247 n n C2 H2 MAN sing 248 n n C3 C4 MAN sing 249 n n C3 O3 MAN sing 250 n n C3 H3 MAN sing 251 n n C4 C5 MAN sing 252 n n C4 O4 MAN sing 253 n n C4 H4 MAN sing 254 n n C5 C6 MAN sing 255 n n C5 O5 MAN sing 256 n n C5 H5 MAN sing 257 n n C6 O6 MAN sing 258 n n C6 H61 MAN sing 259 n n C6 H62 MAN sing 260 n n O1 HO1 MAN sing 261 n n O2 HO2 MAN sing 262 n n O3 HO3 MAN sing 263 n n O4 HO4 MAN sing 264 n n O6 HO6 MAN sing 265 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 2XV7 _atom_sites.fract_transf_matrix[1][1] 0.010447 _atom_sites.fract_transf_matrix[1][2] 0.006032 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012063 _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] 0.014096 _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 3 MAN A 1 403 403 MAN MAN . E 3 MAN A 1 404 404 MAN MAN . F 4 HOH A 1 2001 2001 HOH HOH . F 4 HOH A 2 2002 2002 HOH HOH . F 4 HOH A 3 2003 2003 HOH HOH . F 4 HOH A 4 2004 2004 HOH HOH . F 4 HOH A 5 2005 2005 HOH HOH . F 4 HOH A 6 2006 2006 HOH HOH . F 4 HOH A 7 2007 2007 HOH HOH . F 4 HOH A 8 2008 2008 HOH HOH . F 4 HOH A 9 2009 2009 HOH HOH . F 4 HOH A 10 2010 2010 HOH HOH . F 4 HOH A 11 2011 2011 HOH HOH . F 4 HOH A 12 2012 2012 HOH HOH . F 4 HOH A 13 2013 2013 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 . . . E 3 -33.046 -10.633 -4.552 1 128.28 ? C1 MAN 404 A 1 HETATM 2 C C2 MAN . . . E 3 -32.626 -11.864 -5.348 1 129.35 ? C2 MAN 404 A 1 HETATM 3 C C3 MAN . . . E 3 -31.133 -11.839 -5.668 1 125.49 ? C3 MAN 404 A 1 HETATM 4 C C4 MAN . . . E 3 -30.737 -10.5 -6.252 1 128.46 ? C4 MAN 404 A 1 HETATM 5 C C5 MAN . . . E 3 -31.242 -9.369 -5.371 1 128.12 ? C5 MAN 404 A 1 HETATM 6 C C6 MAN . . . E 3 -31.007 -8.056 -6.082 1 132.55 ? C6 MAN 404 A 1 HETATM 7 O O2 MAN . . . E 3 -33.383 -11.928 -6.537 1 138.49 ? O2 MAN 404 A 1 HETATM 8 O O3 MAN . . . E 3 -30.832 -12.81 -6.634 1 128.42 ? O3 MAN 404 A 1 HETATM 9 O O4 MAN . . . E 3 -29.334 -10.454 -6.379 1 124.25 ? O4 MAN 404 A 1 HETATM 10 O O5 MAN . . . E 3 -32.639 -9.462 -5.214 1 132.33 ? O5 MAN 404 A 1 HETATM 11 O O6 MAN . . . E 3 -32.139 -7.832 -6.889 1 142.23 ? O6 MAN 404 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 11 #