data_6D8D # _model_server_result.job_id MAPFLPYlzzB_lJtFoZ3DSQ _model_server_result.datetime_utc '2024-10-17 21:49:45' _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 6d8d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":401}' # _entry.id 6D8D # _exptl.entry_id 6D8D _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 124.21 _cell.angle_gamma 90 _cell.entry_id 6D8D _cell.length_a 203.571 _cell.length_b 117.866 _cell.length_c 119.86 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D8D _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,Q,R,S _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 L N N ? 5 M N N ? 5 O N N ? 5 P N N ? 5 S 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 GAL NAG C1 O1 . O3 HO3 . sing 2 ? 3 3 1 SIA NAG C2 O2 . O6 HO6 . sing 3 ? 4 2 1 GAL NAG 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 A 409 NAG 3 n G GAL 2 G 2 GAL A 410 GAL 3 n G SIA 3 G 3 SIA A 408 SIA 3 n H NAG 1 H 1 NAG C 409 NAG 3 n H GAL 2 H 2 GAL C 410 GAL 3 n H SIA 3 H 3 SIA C 408 SIA 4 n I NAG 1 I 1 NAG E 409 NAG 4 n I GAL 2 I 2 GAL E 410 GAL # 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 4 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 42 A CYS 42 1_555 A SG CYS 268 A CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? disulf ? disulf3 A SG CYS 54 A CYS 54 1_555 A SG CYS 66 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf4 A SG CYS 87 A CYS 87 1_555 A SG CYS 129 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf5 A SG CYS 272 A CYS 272 1_555 A SG CYS 296 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf7 C SG CYS 4 C CYS 4 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 C SG CYS 42 C CYS 42 1_555 C SG CYS 268 C CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.826 ? disulf ? disulf9 C SG CYS 54 C CYS 54 1_555 C SG CYS 66 C CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.003 ? disulf ? disulf10 C SG CYS 87 C CYS 87 1_555 C SG CYS 129 C CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf11 C SG CYS 272 C CYS 272 1_555 C SG CYS 296 C CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf13 E SG CYS 4 E CYS 4 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf14 E SG CYS 42 E CYS 42 1_555 E SG CYS 268 E CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? disulf ? disulf15 E SG CYS 54 E CYS 54 1_555 E SG CYS 66 E CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf16 E SG CYS 87 E CYS 87 1_555 E SG CYS 129 E CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf17 E SG CYS 272 E CYS 272 1_555 E SG CYS 296 E CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? covale ? covale1 A ND2 ASN 231 A ASN 231 1_555 J C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 B ND2 ASN 82 B ASN 82 1_555 L C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? covale ? covale3 C ND2 ASN 231 C ASN 231 1_555 M C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale4 D ND2 ASN 82 D ASN 82 1_555 O C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale5 E ND2 ASN 231 E ASN 231 1_555 P C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale6 F ND2 ASN 82 F ASN 82 1_555 S C1 NAG . F NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.507 ? covale ? covale7 G O3 NAG . G NAG 1 1_555 G C1 GAL . G GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 sing covale ? covale8 G O6 NAG . G NAG 1 1_555 G C2 SIA . G SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale9 H O3 NAG . H NAG 1 1_555 H C1 GAL . H GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 sing covale ? covale10 H O6 NAG . H NAG 1 1_555 H C2 SIA . H SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale11 I O3 NAG . I NAG 1 1_555 I C1 GAL . I GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 sing # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 6D8D _atom_sites.fract_transf_matrix[1][1] 0.004912 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00334 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008484 _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] 0.010089 _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 1 401 404 NAG NAG . K 6 GAL A 1 405 411 GAL GAL . L 5 NAG B 1 301 201 NAG NAG . M 5 NAG C 1 401 404 NAG NAG . N 6 GAL C 1 405 411 GAL GAL . O 5 NAG D 1 301 201 NAG NAG . P 5 NAG E 1 401 404 NAG NAG . Q 7 SIA E 1 402 408 SIA SIA . R 6 GAL E 1 405 411 GAL GAL . S 5 NAG F 1 301 201 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 13.535 -33.581 -18.801 1 130.17 ? C1 NAG 401 E 1 HETATM 2 C C2 NAG . . . P 5 14.019 -32.603 -17.713 1 134.66 ? C2 NAG 401 E 1 HETATM 3 C C3 NAG . . . P 5 13.055 -31.393 -17.653 1 143.18 ? C3 NAG 401 E 1 HETATM 4 C C4 NAG . . . P 5 12.814 -30.799 -19.073 1 142.49 ? C4 NAG 401 E 1 HETATM 5 C C5 NAG . . . P 5 12.327 -31.88 -20.059 1 137.8 ? C5 NAG 401 E 1 HETATM 6 C C6 NAG . . . P 5 12.067 -31.331 -21.475 1 132.64 ? C6 NAG 401 E 1 HETATM 7 C C7 NAG . . . P 5 13.577 -33.828 -15.479 1 118.95 ? C7 NAG 401 E 1 HETATM 8 C C8 NAG . . . P 5 14.296 -34.499 -14.342 1 116.72 ? C8 NAG 401 E 1 HETATM 9 N N2 NAG . . . P 5 14.371 -33.308 -16.444 1 126.27 ? N2 NAG 401 E 1 HETATM 10 O O3 NAG . . . P 5 13.584 -30.386 -16.768 1 150.7 ? O3 NAG 401 E 1 HETATM 11 O O4 NAG . . . P 5 11.875 -29.702 -19.078 1 139.78 ? O4 NAG 401 E 1 HETATM 12 O O5 NAG . . . P 5 13.298 -32.948 -20.085 1 135.8 ? O5 NAG 401 E 1 HETATM 13 O O6 NAG . . . P 5 10.662 -31.192 -21.748 1 123.66 ? O6 NAG 401 E 1 HETATM 14 O O7 NAG . . . P 5 12.359 -33.781 -15.466 1 113.94 ? O7 NAG 401 E 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 14 #