data_6V80 # _model_server_result.job_id 8WJOtarToj6sTBWwZFdP9A _model_server_result.datetime_utc '2024-10-10 16:30:10' _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 6v80 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":405}' # _entry.id 6V80 # _exptl.entry_id 6V80 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 8 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 6V80 _cell.length_a 210.667 _cell.length_b 165.25 _cell.length_c 84.497 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6V80 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 pentameric 5 author_and_software_defined_assembly 1 PISA pentameric 5 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,B,C,D,E,K,M 1 1 F,G,H,I,J,L,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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 8 O N N ? 8 P N N # _pdbx_entity_branch.entity_id 6 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 6 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 6 n K NAG 1 K 1 NAG A 402 NAG 6 n K NAG 2 K 2 NAG A 403 NAG 6 n L NAG 1 L 1 NAG F 402 NAG 6 n L NAG 2 L 2 NAG F 403 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 99 A CYS 102 1_555 A SG CYS 163 A CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 203 A CYS 206 1_555 A SG CYS 258 A CYS 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 B SG CYS 26 B CYS 25 1_555 B SG CYS 81 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 C SG CYS 25 C CYS 25 1_555 C SG CYS 92 C CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf5 C SG CYS 139 C CYS 139 1_555 C SG CYS 189 C CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf6 C SG CYS 164 C CYS 164 1_555 D SG CYS 168 D CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf7 D SG CYS 21 D CYS 21 1_555 D SG CYS 89 D CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf8 D SG CYS 142 D CYS 142 1_555 D SG CYS 207 D CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf9 E SG CYS 22 E CYS 22 1_555 E SG CYS 95 E CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf10 F SG CYS 99 F CYS 102 1_555 F SG CYS 163 F CYS 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? disulf ? disulf11 F SG CYS 203 F CYS 206 1_555 F SG CYS 258 F CYS 261 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf12 G SG CYS 26 G CYS 25 1_555 G SG CYS 81 G CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf13 H SG CYS 139 H CYS 139 1_555 H SG CYS 189 H CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf14 I SG CYS 21 I CYS 21 1_555 I SG CYS 89 I CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 I SG CYS 142 I CYS 142 1_555 I SG CYS 207 I CYS 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf16 J SG CYS 22 J CYS 22 1_555 J SG CYS 95 J CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 39 A ASN 42 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale2 F ND2 ASN 17 F ASN 20 1_555 P C1 NAG . F NAG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale3 F ND2 ASN 39 F ASN 42 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.519 ? covale ? covale4 F ND2 ASN 160 F ASN 163 1_555 O C1 NAG . F NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.254 ? covale ? covale5 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale6 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 394 n n C1 O1 NAG sing 395 n n C1 O5 NAG sing 396 n n C1 H1 NAG sing 397 n n C2 C3 NAG sing 398 n n C2 N2 NAG sing 399 n n C2 H2 NAG sing 400 n n C3 C4 NAG sing 401 n n C3 O3 NAG sing 402 n n C3 H3 NAG sing 403 n n C4 C5 NAG sing 404 n n C4 O4 NAG sing 405 n n C4 H4 NAG sing 406 n n C5 C6 NAG sing 407 n n C5 O5 NAG sing 408 n n C5 H5 NAG sing 409 n n C6 O6 NAG sing 410 n n C6 H61 NAG sing 411 n n C6 H62 NAG sing 412 n n C7 C8 NAG sing 413 n n C7 N2 NAG sing 414 n n C7 O7 NAG doub 415 n n C8 H81 NAG sing 416 n n C8 H82 NAG sing 417 n n C8 H83 NAG sing 418 n n N2 HN2 NAG sing 419 n n O1 HO1 NAG sing 420 n n O3 HO3 NAG sing 421 n n O4 HO4 NAG sing 422 n n O6 HO6 NAG sing 423 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 6V80 _atom_sites.fract_transf_matrix[1][1] 0.004747 _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] 0.006051 _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] 0.011835 _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 M 7 AGH A 1 401 401 AGH AGH . N 7 AGH F 1 401 401 AGH AGH . O 8 NAG F 1 404 404 NAG NAG . P 8 NAG F 1 405 405 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 8 36.501 16.433 107.988 1 30 ? C1 NAG 405 F 1 HETATM 2 C C2 NAG . . . P 8 35.861 15.109 108.273 1 30 ? C2 NAG 405 F 1 HETATM 3 C C3 NAG . . . P 8 34.555 14.928 107.518 1 30 ? C3 NAG 405 F 1 HETATM 4 C C4 NAG . . . P 8 33.581 16.01 107.879 1 30 ? C4 NAG 405 F 1 HETATM 5 C C5 NAG . . . P 8 34.204 17.32 107.594 1 30 ? C5 NAG 405 F 1 HETATM 6 C C6 NAG . . . P 8 33.318 18.335 108.273 1 30 ? C6 NAG 405 F 1 HETATM 7 C C7 NAG . . . P 8 36.469 12.948 107.684 1 30 ? C7 NAG 405 F 1 HETATM 8 C C8 NAG . . . P 8 35.85 12.666 106.361 1 30 ? C8 NAG 405 F 1 HETATM 9 N N2 NAG . . . P 8 36.849 14.175 107.859 1 30 ? N2 NAG 405 F 1 HETATM 10 O O3 NAG . . . P 8 33.9 13.73 107.901 1 30 ? O3 NAG 405 F 1 HETATM 11 O O4 NAG . . . P 8 32.434 15.909 107.063 1 30 ? O4 NAG 405 F 1 HETATM 12 O O5 NAG . . . P 8 35.432 17.342 108.286 1 30 ? O5 NAG 405 F 1 HETATM 13 O O6 NAG . . . P 8 32.039 18.372 107.656 1 30 ? O6 NAG 405 F 1 HETATM 14 O O7 NAG . . . P 8 36.583 12.132 108.561 1 30 ? O7 NAG 405 F 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 14 #