data_7PEE # _model_server_result.job_id uLXjBrGpaiqYh739RUIMjw _model_server_result.datetime_utc '2025-02-05 05:51:39' _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 7pee # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":301}' # _entry.id 7PEE # _exptl.entry_id 7PEE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method nat _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 7PEE _cell.length_a 145.08 _cell.length_b 145.08 _cell.length_c 217.77 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7PEE _symmetry.cell_setting ? _symmetry.Int_Tables_number 95 _symmetry.space_group_name_Hall 'P 4cw 2c' _symmetry.space_group_name_H-M 'P 43 2 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,G,J,K,N 1 1 B,C,F,H,I,L,M 2 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 I N N ? 4 J 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 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 2 n E NAG 1 E 1 NAG A 269 NAG 2 n E NAG 2 E 2 NAG A 270 NAG 2 n E FUC 3 E 3 FUC A 271 FUC 2 n F NAG 1 F 1 NAG B 270 NAG 2 n F NAG 2 F 2 NAG B 271 NAG 2 n F FUC 3 F 3 FUC B 272 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 4 A CYS 34 1_555 A SG CYS 23 A CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? disulf ? disulf2 A SG CYS 6 A CYS 36 1_555 A SG CYS 36 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 14 A CYS 44 1_555 A SG CYS 25 A CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? disulf ? disulf4 A SG CYS 43 A CYS 73 1_555 A SG CYS 78 A CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 A SG CYS 89 A CYS 119 1_555 A SG CYS 95 A CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 A SG CYS 97 A CYS 127 1_555 A SG CYS 115 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 4 B CYS 34 1_555 B SG CYS 23 B CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf8 B SG CYS 6 B CYS 36 1_555 B SG CYS 36 B CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf9 B SG CYS 14 B CYS 44 1_555 B SG CYS 25 B CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? disulf ? disulf10 B SG CYS 43 B CYS 73 1_555 B SG CYS 78 B CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf11 B SG CYS 89 B CYS 119 1_555 B SG CYS 95 B CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? disulf ? disulf12 B SG CYS 97 B CYS 127 1_555 B SG CYS 115 B CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf13 C SG CYS 4 C CYS 34 1_555 C SG CYS 23 C CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf14 C SG CYS 6 C CYS 36 1_555 C SG CYS 36 C CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf15 C SG CYS 14 C CYS 44 1_555 C SG CYS 25 C CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf16 C SG CYS 43 C CYS 73 1_555 C SG CYS 78 C CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf17 C SG CYS 89 C CYS 119 1_555 C SG CYS 95 C CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf18 C SG CYS 97 C CYS 127 1_555 C SG CYS 115 C CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf19 D SG CYS 4 D CYS 34 1_555 D SG CYS 23 D CYS 53 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf20 D SG CYS 6 D CYS 36 1_555 D SG CYS 36 D CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? disulf ? disulf21 D SG CYS 14 D CYS 44 1_555 D SG CYS 25 D CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? disulf ? disulf22 D SG CYS 43 D CYS 73 1_555 D SG CYS 78 D CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf23 D SG CYS 89 D CYS 119 1_555 D SG CYS 95 D CYS 125 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf24 D SG CYS 97 D CYS 127 1_555 D SG CYS 115 D CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 138 A ASN 168 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale2 B ND2 ASN 138 B ASN 168 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale3 C ND2 ASN 138 C ASN 168 1_555 I C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 D ND2 ASN 138 D ASN 168 1_555 J C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale5 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale6 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale7 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 F O6 NAG . F NAG 1 1_555 F C1 FUC . F FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _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 260 n n C1 O1 NAG sing 261 n n C1 O5 NAG sing 262 n n C1 H1 NAG sing 263 n n C2 C3 NAG sing 264 n n C2 N2 NAG sing 265 n n C2 H2 NAG sing 266 n n C3 C4 NAG sing 267 n n C3 O3 NAG sing 268 n n C3 H3 NAG sing 269 n n C4 C5 NAG sing 270 n n C4 O4 NAG sing 271 n n C4 H4 NAG sing 272 n n C5 C6 NAG sing 273 n n C5 O5 NAG sing 274 n n C5 H5 NAG sing 275 n n C6 O6 NAG sing 276 n n C6 H61 NAG sing 277 n n C6 H62 NAG sing 278 n n C7 C8 NAG sing 279 n n C7 N2 NAG sing 280 n n C7 O7 NAG doub 281 n n C8 H81 NAG sing 282 n n C8 H82 NAG sing 283 n n C8 H83 NAG sing 284 n n N2 HN2 NAG sing 285 n n O1 HO1 NAG sing 286 n n O3 HO3 NAG sing 287 n n O4 HO4 NAG sing 288 n n O6 HO6 NAG sing 289 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 7PEE _atom_sites.fract_transf_matrix[1][1] 0.006893 _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] 0.006893 _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] 0.004592 _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 G 3 SO4 A 1 301 2 SO4 SO4 . H 3 SO4 B 1 301 1 SO4 SO4 . I 4 NAG C 1 301 270 NAG NAG . J 4 NAG D 1 301 269 NAG NAG . K 5 HOH A 1 401 21 HOH HOH . K 5 HOH A 2 402 17 HOH HOH . K 5 HOH A 3 403 14 HOH HOH . K 5 HOH A 4 404 13 HOH HOH . K 5 HOH A 5 405 9 HOH HOH . K 5 HOH A 6 406 16 HOH HOH . K 5 HOH A 7 407 29 HOH HOH . K 5 HOH A 8 408 28 HOH HOH . K 5 HOH A 9 409 30 HOH HOH . K 5 HOH A 10 410 27 HOH HOH . K 5 HOH A 11 411 12 HOH HOH . L 5 HOH B 1 401 19 HOH HOH . L 5 HOH B 2 402 10 HOH HOH . L 5 HOH B 3 403 15 HOH HOH . L 5 HOH B 4 404 22 HOH HOH . L 5 HOH B 5 405 1 HOH HOH . L 5 HOH B 6 406 26 HOH HOH . L 5 HOH B 7 407 2 HOH HOH . L 5 HOH B 8 408 5 HOH HOH . M 5 HOH C 1 401 6 HOH HOH . M 5 HOH C 2 402 3 HOH HOH . M 5 HOH C 3 403 7 HOH HOH . M 5 HOH C 4 404 20 HOH HOH . M 5 HOH C 5 405 18 HOH HOH . M 5 HOH C 6 406 31 HOH HOH . M 5 HOH C 7 407 32 HOH HOH . M 5 HOH C 8 408 24 HOH HOH . M 5 HOH C 9 409 25 HOH HOH . N 5 HOH D 1 401 23 HOH HOH . N 5 HOH D 2 402 11 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 . . . I 4 -33.969 68.848 -76.145 1 117.55 ? C1 NAG 301 C 1 HETATM 2 C C2 NAG . . . I 4 -33.304 70.196 -76.358 1 125.67 ? C2 NAG 301 C 1 HETATM 3 C C3 NAG . . . I 4 -33.491 70.688 -77.788 1 128.96 ? C3 NAG 301 C 1 HETATM 4 C C4 NAG . . . I 4 -33.244 69.577 -78.793 1 126.09 ? C4 NAG 301 C 1 HETATM 5 C C5 NAG . . . I 4 -34.039 68.347 -78.4 1 125.44 ? C5 NAG 301 C 1 HETATM 6 C C6 NAG . . . I 4 -33.896 67.209 -79.399 1 121.34 ? C6 NAG 301 C 1 HETATM 7 C C7 NAG . . . I 4 -33.188 72.118 -74.841 1 125.72 ? C7 NAG 301 C 1 HETATM 8 C C8 NAG . . . I 4 -33.917 72.856 -73.762 1 113.58 ? C8 NAG 301 C 1 HETATM 9 N N2 NAG . . . I 4 -33.879 71.151 -75.433 1 126.93 ? N2 NAG 301 C 1 HETATM 10 O O3 NAG . . . I 4 -32.574 71.752 -78.06 1 126.51 ? O3 NAG 301 C 1 HETATM 11 O O4 NAG . . . I 4 -33.649 70.028 -80.084 1 127.63 ? O4 NAG 301 C 1 HETATM 12 O O5 NAG . . . I 4 -33.536 67.937 -77.141 1 119.07 ? O5 NAG 301 C 1 HETATM 13 O O6 NAG . . . I 4 -34.669 67.49 -80.57 1 113.23 ? O6 NAG 301 C 1 HETATM 14 O O7 NAG . . . I 4 -32.043 72.398 -75.148 1 128.3 ? O7 NAG 301 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #