data_8DVN # _model_server_result.job_id S9p2Xr7lZW_njJs2l32eiQ _model_server_result.datetime_utc '2024-11-25 14:11:10' _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 8dvn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1301}' # _entry.id 8DVN # _exptl.entry_id 8DVN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 8DVN _cell.length_a 68.097 _cell.length_b 116.783 _cell.length_c 127.164 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DVN _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,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 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide 5 oligosaccharide 6 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 3 1 FUC NAG C1 O1 . O6 HO6 . sing 5 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 6 2 1 NAG 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 C NAG 1 C 1 NAG A 1250 NAG 3 n C NAG 2 C 2 NAG A 1251 NAG 3 n C BMA 3 C 3 BMA A 1252 BMA 4 n D NAG 1 D 1 NAG A 1253 NAG 4 n D NAG 2 D 2 NAG A 1254 NAG 4 n D FUC 3 D 3 FUC A 1260 FUC 5 n E NAG 1 E 1 NAG A 1255 NAG 5 n E NAG 2 E 2 NAG A 1256 NAG 6 n F NAG 1 F 1 NAG A 1257 NAG 6 n F NAG 2 F 2 NAG A 1258 NAG # 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 264 A CYS 893 1_555 A SG CYS 275 A CYS 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 271 A CYS 900 1_555 A SG CYS 285 A CYS 914 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 287 A CYS 916 1_555 A SG CYS 300 A CYS 929 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf4 A SG CYS 578 A CYS 1207 1_555 A SG CYS 589 A CYS 1218 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 585 A CYS 1214 1_555 A SG CYS 599 A CYS 1228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 601 A CYS 1230 1_555 A SG CYS 614 A CYS 1243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 2 B CYS 2 1_555 B SG CYS 31 B CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 B SG CYS 13 B CYS 13 1_555 B SG CYS 25 B CYS 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf9 B SG CYS 19 B CYS 19 1_555 B SG CYS 23 B CYS 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 63 A ASN 692 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale2 A ND2 ASN 230 A ASN 859 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale3 A ND2 ASN 236 A ASN 865 1_555 G C1 NAG . A NAG 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 A ND2 ASN 297 A ASN 926 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale5 A C THR 402 A THR 1031 1_555 A N OCS 403 A OCS 1032 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale6 A C OCS 403 A OCS 1032 1_555 A N GLU 404 A GLU 1033 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale7 A ND2 ASN 410 A ASN 1039 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale8 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale9 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale10 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale11 D O6 NAG . D NAG 1 1_555 D C1 FUC . D FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale12 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale13 F O6 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? metalc ? metalc1 A O THR 95 A THR 724 1_555 I CA CA . A CA 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc2 A OD1 ASN 98 A ASN 727 1_555 I CA CA . A CA 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc3 A OG SER 120 A SER 749 1_555 I CA CA . A CA 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.825 ? metalc ? metalc4 A O LEU 209 A LEU 838 1_555 H CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc5 A OD1 ASP 249 A ASP 878 1_555 H CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.052 ? metalc ? metalc6 A O ILE 250 A ILE 879 1_555 H CA CA . A CA 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc7 A OD2 ASP 389 A ASP 1018 1_555 J CA CA . A CA 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? metalc ? metalc8 A O LEU 390 A LEU 1019 1_555 J CA CA . A CA 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.067 ? metalc ? metalc9 A O ILE 433 A ILE 1062 1_555 J CA CA . A CA 1304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc10 A O LEU 521 A LEU 1150 1_555 K CA CA . A CA 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.007 ? metalc ? metalc11 A OD1 ASP 561 A ASP 1190 1_555 K CA CA . A CA 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? metalc ? metalc12 A O ILE 562 A ILE 1191 1_555 K CA CA . A CA 1305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? # _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 284 n n C1 O1 NAG sing 285 n n C1 O5 NAG sing 286 n n C1 H1 NAG sing 287 n n C2 C3 NAG sing 288 n n C2 N2 NAG sing 289 n n C2 H2 NAG sing 290 n n C3 C4 NAG sing 291 n n C3 O3 NAG sing 292 n n C3 H3 NAG sing 293 n n C4 C5 NAG sing 294 n n C4 O4 NAG sing 295 n n C4 H4 NAG sing 296 n n C5 C6 NAG sing 297 n n C5 O5 NAG sing 298 n n C5 H5 NAG sing 299 n n C6 O6 NAG sing 300 n n C6 H61 NAG sing 301 n n C6 H62 NAG sing 302 n n C7 C8 NAG sing 303 n n C7 N2 NAG sing 304 n n C7 O7 NAG doub 305 n n C8 H81 NAG sing 306 n n C8 H82 NAG sing 307 n n C8 H83 NAG sing 308 n n N2 HN2 NAG sing 309 n n O1 HO1 NAG sing 310 n n O3 HO3 NAG sing 311 n n O4 HO4 NAG sing 312 n n O6 HO6 NAG sing 313 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 8DVN _atom_sites.fract_transf_matrix[1][1] 0.014685 _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] 0.008563 _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 G 7 NAG A 1 1301 1259 NAG NAG . H 8 CA A 1 1302 1 CA CA . I 8 CA A 1 1303 2 CA CA . J 8 CA A 1 1304 3 CA CA . K 8 CA A 1 1305 4 CA CA . L 9 HOH A 1 1401 9 HOH HOH . L 9 HOH A 2 1402 7 HOH HOH . L 9 HOH A 3 1403 1 HOH HOH . L 9 HOH A 4 1404 4 HOH HOH . L 9 HOH A 5 1405 8 HOH HOH . L 9 HOH A 6 1406 2 HOH HOH . L 9 HOH A 7 1407 5 HOH HOH . L 9 HOH A 8 1408 6 HOH HOH . M 9 HOH B 1 101 3 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 7 -0.683 45.483 29.712 1 136.54 ? C1 NAG 1301 A 1 HETATM 2 C C2 NAG . . . G 7 -2.137 45.283 30.109 1 134.44 ? C2 NAG 1301 A 1 HETATM 3 C C3 NAG . . . G 7 -2.277 45.219 31.624 1 139.64 ? C3 NAG 1301 A 1 HETATM 4 C C4 NAG . . . G 7 -1.337 46.189 32.332 1 142.01 ? C4 NAG 1301 A 1 HETATM 5 C C5 NAG . . . G 7 0.102 46.02 31.852 1 136.32 ? C5 NAG 1301 A 1 HETATM 6 C C6 NAG . . . G 7 1.031 45.501 32.935 1 126.21 ? C6 NAG 1301 A 1 HETATM 7 C C7 NAG . . . G 7 -4.19 46.227 29.255 1 132.06 ? C7 NAG 1301 A 1 HETATM 8 C C8 NAG . . . G 7 -4.837 47.414 28.608 1 117.79 ? C8 NAG 1301 A 1 HETATM 9 N N2 NAG . . . G 7 -2.92 46.384 29.599 1 134.64 ? N2 NAG 1301 A 1 HETATM 10 O O3 NAG . . . G 7 -2.022 43.883 32.066 1 139.25 ? O3 NAG 1301 A 1 HETATM 11 O O4 NAG . . . G 7 -1.774 47.537 32.114 1 130.96 ? O4 NAG 1301 A 1 HETATM 12 O O5 NAG . . . G 7 0.145 45.081 30.791 1 137.02 ? O5 NAG 1301 A 1 HETATM 13 O O6 NAG . . . G 7 0.97 44.074 32.908 1 126.31 ? O6 NAG 1301 A 1 HETATM 14 O O7 NAG . . . G 7 -4.789 45.184 29.447 1 128.45 ? O7 NAG 1301 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 14 #