data_1RD8 # _model_server_result.job_id hlTLQciuzMV0JOTvEd3jKw _model_server_result.datetime_utc '2024-11-24 06:55:37' _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 1rd8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":330}' # _entry.id 1RD8 # _exptl.entry_id 1RD8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 108.63 _cell.angle_gamma 90 _cell.entry_id 1RD8 _cell.length_a 190.529 _cell.length_b 109.953 _cell.length_c 136.238 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1RD8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_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,N,O,P _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 ? 5 J N N ? 5 K N N ? 5 L N N ? 5 N N N ? 5 O N N ? 5 P N 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 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 5 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . 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 G NAG 1 G 1 NAG G 3 NAG 3 n G NAG 2 G 2 NAG G 4 NAG 3 n G BMA 3 G 3 BMA G 5 MAN 4 n H NAG 1 H 1 NAG H 2 NAG 4 n H NAG 2 H 2 NAG H 3 NAG 4 n H BMA 3 H 3 BMA H 4 MAN 4 n H MAN 4 H 4 MAN H 5 MAN 3 n I NAG 1 I 1 NAG I 2 NAG 3 n I NAG 2 I 2 NAG I 3 NAG 3 n I BMA 3 I 3 BMA I 4 MAN # 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 12 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? disulf ? disulf2 A SG CYS 50 A CYS 52 1_555 A SG CYS 283 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? disulf ? disulf3 A SG CYS 63 A CYS 64 1_555 A SG CYS 75 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf4 A SG CYS 98 A CYS 97 1_555 A SG CYS 144 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? disulf ? disulf5 A SG CYS 287 A CYS 281 1_555 A SG CYS 311 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? disulf ? disulf7 C SG CYS 12 C CYS 14 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? disulf ? disulf8 C SG CYS 50 C CYS 52 1_555 C SG CYS 283 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? disulf ? disulf9 C SG CYS 63 C CYS 64 1_555 C SG CYS 75 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf10 C SG CYS 98 C CYS 97 1_555 C SG CYS 144 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf11 C SG CYS 287 C CYS 281 1_555 C SG CYS 311 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? disulf ? disulf13 E SG CYS 12 E CYS 14 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? disulf ? disulf14 E SG CYS 50 E CYS 52 1_555 E SG CYS 283 E CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? disulf ? disulf15 E SG CYS 63 E CYS 64 1_555 E SG CYS 75 E CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf16 E SG CYS 98 E CYS 97 1_555 E SG CYS 144 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? disulf ? disulf17 E SG CYS 287 E CYS 281 1_555 E SG CYS 311 E CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? covale ? covale1 J C1 NAG . A NAG 1 1_555 A ND2 ASN 19 A ASN 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale2 K C1 NAG . A NAG 2 1_555 A ND2 ASN 31 A ASN 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 A ND2 ASN 95 A ASN 95 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 A C ARG 335 A ARG 329 1_555 B N GLY 1 B GLY 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale5 B ND2 ASN 154 B ASN 154 1_555 L C1 NAG . B NAG 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale6 C ND2 ASN 31 C ASN 34 1_555 N C1 NAG . C NAG 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale7 C ND2 ASN 95 C ASN 95 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale8 C ND2 ASN 295 C ASN 289 1_555 O C1 NAG . C NAG 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale9 C C ARG 335 C ARG 329 1_555 D N GLY 1 D GLY 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale10 E ND2 ASN 31 E ASN 34 1_555 P C1 NAG . E NAG 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale11 E ND2 ASN 95 E ASN 95 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale12 E C ARG 335 E ARG 329 1_555 F N GLY 1 F GLY 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale13 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale14 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale15 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale16 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale17 H O3 BMA . H BMA 3 1_555 H C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale18 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale19 I O4 NAG . I NAG 2 1_555 I C1 BMA . I BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 1RD8 _atom_sites.fract_transf_matrix[1][1] 0.005249 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001769 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009095 _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] 0.007746 _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 J 5 NAG A 1 1 1 NAG NAG . K 5 NAG A 1 2 2 NAG NAG . L 5 NAG B 1 183 6 NAG NAG . M 6 PO4 B 1 301 1 PO4 PO4 . N 5 NAG C 1 330 1 NAG NAG . O 5 NAG C 1 335 6 NAG NAG . P 5 NAG E 1 330 1 NAG NAG . # 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 5 54.005 20.444 79.32 1 64.34 ? C1 NAG 330 E 1 HETATM 2 C C2 NAG . . . P 5 53.296 21.833 79.325 1 69.25 ? C2 NAG 330 E 1 HETATM 3 C C3 NAG . . . P 5 53.707 22.445 77.935 1 68.69 ? C3 NAG 330 E 1 HETATM 4 C C4 NAG . . . P 5 55.25 22.642 77.993 1 66.49 ? C4 NAG 330 E 1 HETATM 5 C C5 NAG . . . P 5 56.046 21.459 78.623 1 66.02 ? C5 NAG 330 E 1 HETATM 6 C C6 NAG . . . P 5 57.362 21.828 79.306 1 65.58 ? C6 NAG 330 E 1 HETATM 7 C C7 NAG . . . P 5 50.969 22.706 79.975 1 70.88 ? C7 NAG 330 E 1 HETATM 8 C C8 NAG . . . P 5 50.391 23.486 78.81 1 70.57 ? C8 NAG 330 E 1 HETATM 9 N N2 NAG . . . P 5 51.853 21.727 79.705 1 71.13 ? N2 NAG 330 E 1 HETATM 10 O O3 NAG . . . P 5 52.909 23.518 77.399 1 67.46 ? O3 NAG 330 E 1 HETATM 11 O O4 NAG . . . P 5 55.692 22.834 76.685 1 63.28 ? O4 NAG 330 E 1 HETATM 12 O O5 NAG . . . P 5 55.336 20.749 79.637 1 65.36 ? O5 NAG 330 E 1 HETATM 13 O O6 NAG . . . P 5 57.765 20.673 80.036 1 63.88 ? O6 NAG 330 E 1 HETATM 14 O O7 NAG . . . P 5 50.594 22.917 81.135 1 69.41 ? O7 NAG 330 E 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #