data_8JR3 # _model_server_result.job_id SgBFbXT14GYrjxrr7NRgaA _model_server_result.datetime_utc '2024-11-16 08:35:38' _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 8jr3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":701}' # _entry.id 8JR3 # _exptl.entry_id 8JR3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 8 _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 8JR3 _cell.length_a 110.843 _cell.length_b 257.014 _cell.length_c 193.518 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8JR3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,E,F,G,H,I,J,K 1 1 B,C,D,L,M,N,O,P 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 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id P _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 4 oligosaccharide 5 oligosaccharide 6 oligosaccharide 7 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 5 3 1 FUC NAG C1 O1 . O6 HO6 . sing 5 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 7 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 7 3 2 BMA NAG C1 O1 . O4 HO4 . sing 8 ? 7 4 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 4 n G NAG 1 G 1 NAG G 1 NAG 4 n G NAG 2 G 2 NAG G 2 NAG 4 n G BMA 3 G 3 BMA G 3 BMA 5 n H NAG 1 H 1 NAG H 1 NAG 5 n H NAG 2 H 2 NAG H 2 NAG 5 n H FUC 3 H 3 FUC H 3 FUC 6 n I NAG 1 I 1 NAG I 1 NAG 6 n I NAG 2 I 2 NAG I 2 NAG 6 n J NAG 1 J 1 NAG J 1 NAG 6 n J NAG 2 J 2 NAG J 2 NAG 7 n K NAG 1 K 1 NAG K 1 NAG 7 n K NAG 2 K 2 NAG K 2 NAG 7 n K BMA 3 K 3 BMA K 3 BMA 7 n K FUC 4 K 4 FUC K 4 FUC 6 n L NAG 1 L 1 NAG L 1 NAG 6 n L NAG 2 L 2 NAG L 2 NAG 6 n M NAG 1 M 1 NAG M 1 NAG 6 n M NAG 2 M 2 NAG M 2 NAG 5 n N NAG 1 N 1 NAG N 1 NAG 5 n N NAG 2 N 2 NAG N 2 NAG 5 n N FUC 3 N 3 FUC N 3 FUC 5 n O NAG 1 O 1 NAG O 1 NAG 5 n O NAG 2 O 2 NAG O 2 NAG 5 n O FUC 3 O 3 FUC O 3 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 2 E CYS 189 1_555 A SG CYS 414 E CYS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 29 E CYS 216 1_555 A SG CYS 53 E CYS 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 195 E CYS 382 1_555 A SG CYS 208 E CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 A SG CYS 200 E CYS 387 1_555 A SG CYS 312 E CYS 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 306 E CYS 493 1_555 A SG CYS 316 E CYS 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? disulf ? disulf6 A SG CYS 378 E CYS 565 1_555 A SG CYS 387 E CYS 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 B SG CYS 2 F CYS 189 1_555 B SG CYS 414 F CYS 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf8 B SG CYS 29 F CYS 216 1_555 B SG CYS 53 F CYS 240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 B SG CYS 95 F CYS 282 1_555 B SG CYS 108 F CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf10 B SG CYS 195 F CYS 382 1_555 B SG CYS 208 F CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf11 B SG CYS 200 F CYS 387 1_555 B SG CYS 312 F CYS 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf12 B SG CYS 306 F CYS 493 1_555 B SG CYS 316 F CYS 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf13 B SG CYS 378 F CYS 565 1_555 B SG CYS 387 F CYS 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf14 C SG CYS 22 A CYS 22 1_555 C SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf15 C SG CYS 143 A CYS 143 1_555 C SG CYS 199 A CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf16 D SG CYS 23 D CYS 23 1_555 D SG CYS 93 D CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 D SG CYS 139 D CYS 139 1_555 D SG CYS 199 D CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf18 E SG CYS 22 B CYS 22 1_555 E SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf19 E SG CYS 143 B CYS 143 1_555 E SG CYS 199 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf20 F SG CYS 23 C CYS 23 1_555 F SG CYS 93 C CYS 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf21 F SG CYS 139 C CYS 139 1_555 F SG CYS 199 C CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? covale ? covale1 A ND2 ASN 119 E ASN 306 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale2 A ND2 ASN 191 E ASN 378 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale3 A ND2 ASN 230 E ASN 417 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale4 A ND2 ASN 294 E ASN 481 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 A ND2 ASN 342 E ASN 529 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale6 B ND2 ASN 119 F ASN 306 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale7 B ND2 ASN 191 F ASN 378 1_555 P C1 NAG . F NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale8 B ND2 ASN 230 F ASN 417 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale9 B ND2 ASN 294 F ASN 481 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale10 B ND2 ASN 342 F ASN 529 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 ? covale ? covale11 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale12 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale13 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale14 H O6 NAG . H NAG 1 1_555 H C1 FUC . H FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale15 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale16 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale17 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale18 K O6 NAG . K NAG 1 1_555 K C1 FUC . K FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale19 K O4 NAG . K NAG 2 1_555 K C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale20 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale21 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale22 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale23 N O6 NAG . N NAG 1 1_555 N C1 FUC . N FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale24 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale25 O O6 NAG . O NAG 1 1_555 O C1 FUC . O FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? # _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 282 n n C1 O1 NAG sing 283 n n C1 O5 NAG sing 284 n n C1 H1 NAG sing 285 n n C2 C3 NAG sing 286 n n C2 N2 NAG sing 287 n n C2 H2 NAG sing 288 n n C3 C4 NAG sing 289 n n C3 O3 NAG sing 290 n n C3 H3 NAG sing 291 n n C4 C5 NAG sing 292 n n C4 O4 NAG sing 293 n n C4 H4 NAG sing 294 n n C5 C6 NAG sing 295 n n C5 O5 NAG sing 296 n n C5 H5 NAG sing 297 n n C6 O6 NAG sing 298 n n C6 H61 NAG sing 299 n n C6 H62 NAG sing 300 n n C7 C8 NAG sing 301 n n C7 N2 NAG sing 302 n n C7 O7 NAG doub 303 n n C8 H81 NAG sing 304 n n C8 H82 NAG sing 305 n n C8 H83 NAG sing 306 n n N2 HN2 NAG sing 307 n n O1 HO1 NAG sing 308 n n O3 HO3 NAG sing 309 n n O4 HO4 NAG sing 310 n n O6 HO6 NAG sing 311 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 8JR3 _atom_sites.fract_transf_matrix[1][1] 0.009022 _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] 0.003891 _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] 0.005167 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id P _pdbx_nonpoly_scheme.entity_id 8 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id F _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 701 _pdbx_nonpoly_scheme.auth_seq_num 617 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . P 8 -50.785 15.491 -34.675 1 124.98 ? C1 NAG 701 F 1 HETATM 2 C C2 NAG . . . P 8 -51.685 15.315 -35.897 1 117.8 ? C2 NAG 701 F 1 HETATM 3 C C3 NAG . . . P 8 -53.121 15.066 -35.454 1 108.11 ? C3 NAG 701 F 1 HETATM 4 C C4 NAG . . . P 8 -53.178 13.867 -34.519 1 104.58 ? C4 NAG 701 F 1 HETATM 5 C C5 NAG . . . P 8 -52.217 14.057 -33.348 1 116.35 ? C5 NAG 701 F 1 HETATM 6 C C6 NAG . . . P 8 -52.12 12.826 -32.477 1 91.6 ? C6 NAG 701 F 1 HETATM 7 C C7 NAG . . . P 8 -50.943 16.425 -37.948 1 109.61 ? C7 NAG 701 F 1 HETATM 8 C C8 NAG . . . P 8 -50.962 17.686 -38.757 1 95.53 ? C8 NAG 701 F 1 HETATM 9 N N2 NAG . . . P 8 -51.609 16.46 -36.79 1 116.28 ? N2 NAG 701 F 1 HETATM 10 O O3 NAG . . . P 8 -53.942 14.831 -36.593 1 101.35 ? O3 NAG 701 F 1 HETATM 11 O O4 NAG . . . P 8 -54.499 13.715 -34.012 1 95.54 ? O4 NAG 701 F 1 HETATM 12 O O5 NAG . . . P 8 -50.889 14.329 -33.826 1 142.52 ? O5 NAG 701 F 1 HETATM 13 O O6 NAG . . . P 8 -51.307 13.057 -31.335 1 77.26 ? O6 NAG 701 F 1 HETATM 14 O O7 NAG . . . P 8 -50.349 15.417 -38.325 1 106.58 ? O7 NAG 701 F 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #