data_7URU # _model_server_result.job_id 7X3mYWQYPVjaE3zk04zBfg _model_server_result.datetime_utc '2024-11-28 05:32:28' _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 7uru # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1002}' # _entry.id 7URU # _exptl.entry_id 7URU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 7URU _cell.length_a 72.983 _cell.length_b 100.75 _cell.length_c 124.916 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7URU _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_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 # _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 ? 4 F N N ? 4 G N N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 3 6 3 MAN BMA C1 O1 . O6 HO6 . sing 6 ? 3 7 6 NAG MAN C1 O1 . O2 HO2 . sing 7 ? 3 8 1 FUC NAG C1 O1 . O6 HO6 . 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 3 n D NAG 1 D 1 NAG A 1001 NAG 3 n D NAG 2 D 2 NAG A 1002 NAG 3 n D BMA 3 D 3 BMA A 1003 BMA 3 n D MAN 4 D 4 MAN A 1004 MAN 3 n D NAG 5 D 5 NAG A 1005 NAG 3 n D MAN 6 D 6 MAN A 1006 MAN 3 n D NAG 7 D 7 NAG A 1007 NAG 3 n D FUC 8 D 8 FUC A 1009 FUC 3 n E NAG 1 E 1 NAG B 1001 NAG 3 n E NAG 2 E 2 NAG B 1002 NAG 3 n E BMA 3 E 3 BMA B 1003 BMA 3 n E MAN 4 E 4 MAN B 1004 MAN 3 n E NAG 5 E 5 NAG B 1005 NAG 3 n E MAN 6 E 6 MAN B 1006 MAN 3 n E NAG 7 E 7 NAG B 1007 NAG 3 n E FUC 8 E 8 FUC B 1009 FUC # 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 37 A CYS 261 1_555 A SG CYS 97 A CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf2 A SG CYS 143 A CYS 367 1_555 A SG CYS 201 A CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf3 B SG CYS 37 B CYS 261 1_555 B SG CYS 97 B CYS 321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf4 B SG CYS 143 B CYS 367 1_555 B SG CYS 201 B CYS 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf5 C SG CYS 31 C CYS 29 1_555 C SG CYS 73 C CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf6 C SG CYS 112 C CYS 110 1_555 C SG CYS 156 C CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? covale ? covale1 A ND2 ASN 73 A ASN 297 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 B ND2 ASN 73 B ASN 297 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 C ND2 ASN 47 C ASN 45 1_555 G C1 NAG . C NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale4 C ND2 ASN 164 C ASN 162 1_555 F C1 NAG . C NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale6 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale7 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale8 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 D O2 MAN . D MAN 4 1_555 D C1 NAG . D NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale11 D O2 MAN . D MAN 6 1_555 D C1 NAG . D NAG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale13 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale14 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale15 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale16 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale17 E O2 MAN . E MAN 4 1_555 E C1 NAG . E NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale18 E O2 MAN . E MAN 6 1_555 E C1 NAG . E NAG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 308 n n C1 O1 NAG sing 309 n n C1 O5 NAG sing 310 n n C1 H1 NAG sing 311 n n C2 C3 NAG sing 312 n n C2 N2 NAG sing 313 n n C2 H2 NAG sing 314 n n C3 C4 NAG sing 315 n n C3 O3 NAG sing 316 n n C3 H3 NAG sing 317 n n C4 C5 NAG sing 318 n n C4 O4 NAG sing 319 n n C4 H4 NAG sing 320 n n C5 C6 NAG sing 321 n n C5 O5 NAG sing 322 n n C5 H5 NAG sing 323 n n C6 O6 NAG sing 324 n n C6 H61 NAG sing 325 n n C6 H62 NAG sing 326 n n C7 C8 NAG sing 327 n n C7 N2 NAG sing 328 n n C7 O7 NAG doub 329 n n C8 H81 NAG sing 330 n n C8 H82 NAG sing 331 n n C8 H83 NAG sing 332 n n N2 HN2 NAG sing 333 n n O1 HO1 NAG sing 334 n n O3 HO3 NAG sing 335 n n O4 HO4 NAG sing 336 n n O6 HO6 NAG sing 337 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 NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 7URU _atom_sites.fract_transf_matrix[1][1] 0.013702 _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] 0.009926 _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] 0.008005 _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 F 4 NAG C 1 1001 1001 NAG NAG . G 4 NAG C 1 1002 1003 NAG NAG . H 5 HOH A 1 501 3 HOH HOH . H 5 HOH A 2 502 13 HOH HOH . H 5 HOH A 3 503 7 HOH HOH . H 5 HOH A 4 504 1 HOH HOH . H 5 HOH A 5 505 9 HOH HOH . I 5 HOH B 1 501 6 HOH HOH . I 5 HOH B 2 502 2 HOH HOH . I 5 HOH B 3 503 12 HOH HOH . I 5 HOH B 4 504 5 HOH HOH . I 5 HOH B 5 505 14 HOH HOH . J 5 HOH C 1 1101 8 HOH HOH . J 5 HOH C 2 1102 4 HOH HOH . J 5 HOH C 3 1103 11 HOH HOH . J 5 HOH C 4 1104 10 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 NAG . . . G 4 -11.412 -3.245 58.482 1 72.15 ? C1 NAG 1002 C 1 HETATM 2 C C2 NAG . . . G 4 -12.678 -3.202 57.646 1 69.88 ? C2 NAG 1002 C 1 HETATM 3 C C3 NAG . . . G 4 -12.419 -3.824 56.286 1 69.34 ? C3 NAG 1002 C 1 HETATM 4 C C4 NAG . . . G 4 -11.216 -3.171 55.623 1 61.19 ? C4 NAG 1002 C 1 HETATM 5 C C5 NAG . . . G 4 -10.027 -3.206 56.571 1 74.62 ? C5 NAG 1002 C 1 HETATM 6 C C6 NAG . . . G 4 -8.809 -2.49 56.03 1 74.89 ? C6 NAG 1002 C 1 HETATM 7 C C7 NAG . . . G 4 -14.648 -3.263 59.111 1 86.83 ? C7 NAG 1002 C 1 HETATM 8 C C8 NAG . . . G 4 -15.738 -4.114 59.691 1 75.63 ? C8 NAG 1002 C 1 HETATM 9 N N2 NAG . . . G 4 -13.777 -3.886 58.309 1 78.37 ? N2 NAG 1002 C 1 HETATM 10 O O3 NAG . . . G 4 -13.582 -3.705 55.476 1 79.24 ? O3 NAG 1002 C 1 HETATM 11 O O4 NAG . . . G 4 -10.876 -3.912 54.458 1 83.86 ? O4 NAG 1002 C 1 HETATM 12 O O5 NAG . . . G 4 -10.382 -2.573 57.811 1 66.42 ? O5 NAG 1002 C 1 HETATM 13 O O6 NAG . . . G 4 -9.044 -1.095 55.898 1 77.04 ? O6 NAG 1002 C 1 HETATM 14 O O7 NAG . . . G 4 -14.558 -2.065 59.357 1 81.11 ? O7 NAG 1002 C 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 322 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #