data_2GY7 # _model_server_result.job_id lR_yJTyK1tqX4KQdEVxkBg _model_server_result.datetime_utc '2024-12-21 12:57:48' _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 2gy7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1140}' # _entry.id 2GY7 # _exptl.entry_id 2GY7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _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 2GY7 _cell.length_a 165.636 _cell.length_b 165.636 _cell.length_c 115.31 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GY7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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 6 _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 # 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 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 NDG NAG C1 O1 . O4 HO4 . sing 4 ? 4 2 1 NAG 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 3 n C NAG 1 C 1 NAG C 1158 NAG 3 n C NAG 2 C 2 NAG C 1159 NAG 3 n C NAG 3 C 3 NAG C 1160 NAG 3 n C NDG 4 C 4 NDG C 1161 NAG 4 n D NAG 1 D 1 NAG D 1399 NAG 4 n D NAG 2 D 2 NAG D 1400 NAG 4 n E NAG 1 E 1 NAG E 1438 NAG 4 n E NAG 2 E 2 NAG E 1439 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 5 A CYS 284 1_555 A SG CYS 34 A CYS 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 154 A CYS 433 1_555 A SG CYS 156 A CYS 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 158 A CYS 437 1_555 A SG CYS 171 A CYS 450 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 22 B CYS 44 1_555 B SG CYS 80 B CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 B SG CYS 189 B CYS 211 1_555 B SG CYS 198 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 B SG CYS 202 B CYS 224 1_555 B SG CYS 211 B CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf7 B SG CYS 205 B CYS 227 1_555 B SG CYS 218 B CYS 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 220 B CYS 242 1_555 B SG CYS 229 B CYS 251 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 B SG CYS 233 B CYS 255 1_555 B SG CYS 242 B CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf10 B SG CYS 246 B CYS 268 1_555 B SG CYS 252 B CYS 274 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf11 B SG CYS 258 B CYS 280 1_555 B SG CYS 265 B CYS 287 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf12 B SG CYS 267 B CYS 289 1_555 B SG CYS 276 B CYS 298 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 B SG CYS 280 B CYS 302 1_555 B SG CYS 289 B CYS 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf14 B SG CYS 293 B CYS 315 1_555 B SG CYS 301 B CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf15 B SG CYS 295 B CYS 317 1_555 B SG CYS 307 B CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf16 B SG CYS 309 B CYS 331 1_555 B SG CYS 318 B CYS 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf17 B SG CYS 348 B CYS 370 1_555 B SG CYS 402 B CYS 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 B OD1 ASN 118 B ASN 140 1_555 G C1 NAG . B NAG 1140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? covale ? covale2 B ND2 ASN 136 B ASN 158 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? covale ? covale3 B ND2 ASN 377 B ASN 399 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.049 ? covale ? covale4 B ND2 ASN 377 B ASN 399 1_555 D C2 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.815 ? covale ? covale5 B ND2 ASN 416 B ASN 438 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.829 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 NAG . C NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale8 C O4 NAG . C NAG 3 1_555 C C1 NDG . C NDG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? metalc ? metalc1 F CA CA . A CA 1 1_555 A OD1 ASP 150 A ASP 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc2 F CA CA . A CA 1 1_555 A OD2 ASP 150 A ASP 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc3 F CA CA . A CA 1 1_555 A OD1 ASP 152 A ASP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.08 ? metalc ? metalc4 F CA CA . A CA 1 1_555 A OD2 ASP 152 A ASP 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.711 ? metalc ? metalc5 F CA CA . A CA 1 1_555 A O CYS 154 A CYS 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.384 ? metalc ? metalc6 F CA CA . A CA 1 1_555 A O CYS 156 A CYS 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? # _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 ? # 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 2GY7 _atom_sites.fract_transf_matrix[1][1] 0.006037 _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] 0.006037 _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] 0.008672 _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 5 CA A 1 1 1 CA CA . G 6 NAG B 1 1140 1140 NAG NAG . H 7 SO4 B 1 3 3 SO4 SO4 . I 7 SO4 B 1 4 4 SO4 SO4 . # 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 6 52.232 37.447 30.665 1 34.51 ? C1 NAG 1140 B 1 HETATM 2 C C2 NAG . . . G 6 52.209 38.276 29.368 1 37.6 ? C2 NAG 1140 B 1 HETATM 3 C C3 NAG . . . G 6 53.638 38.473 28.798 1 39.71 ? C3 NAG 1140 B 1 HETATM 4 C C4 NAG . . . G 6 54.665 38.871 29.876 1 38.93 ? C4 NAG 1140 B 1 HETATM 5 C C5 NAG . . . G 6 54.536 37.98 31.111 1 40 ? C5 NAG 1140 B 1 HETATM 6 C C6 NAG . . . G 6 55.444 38.442 32.245 1 39.98 ? C6 NAG 1140 B 1 HETATM 7 C C7 NAG . . . G 6 50.88 38.301 27.349 1 39.4 ? C7 NAG 1140 B 1 HETATM 8 C C8 NAG . . . G 6 51.518 38.086 25.984 1 39.81 ? C8 NAG 1140 B 1 HETATM 9 N N2 NAG . . . G 6 51.373 37.614 28.377 1 39.61 ? N2 NAG 1140 B 1 HETATM 10 O O3 NAG . . . G 6 53.593 39.482 27.793 1 41.48 ? O3 NAG 1140 B 1 HETATM 11 O O4 NAG . . . G 6 55.987 38.765 29.362 1 37.42 ? O4 NAG 1140 B 1 HETATM 12 O O5 NAG . . . G 6 53.176 38.004 31.603 1 38.32 ? O5 NAG 1140 B 1 HETATM 13 O O6 NAG . . . G 6 55.106 39.754 32.683 1 43.22 ? O6 NAG 1140 B 1 HETATM 14 O O7 NAG . . . G 6 49.942 39.089 27.468 1 41.33 ? O7 NAG 1140 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 503 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #