data_7PKI # _model_server_result.job_id y054g1cBAOp4uDTb00zeGA _model_server_result.datetime_utc '2024-10-11 23:20:58' _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 7pki # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":1701}' # _entry.id 7PKI # _exptl.entry_id 7PKI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _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 90 _cell.angle_gamma 120 _cell.entry_id 7PKI _cell.length_a 341.535 _cell.length_b 341.535 _cell.length_c 68.153 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7PKI _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall 'P 65 2 (x,y,z+1/12)' _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,T,U,V,W,X,Y _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 ? 4 D N N ? 4 E N N ? 4 F N N ? 4 G N N ? 4 O N N ? 4 P N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 3 n C NAG 1 B 1 NAG A 1075 NAG 3 n C NAG 2 B 2 NAG A 1076 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 115 A CYS 133 1_555 A SG CYS 123 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 326 A CYS 344 1_555 A SG CYS 343 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 512 A CYS 530 1_555 A SG CYS 524 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 B SG CYS 5 E CYS 332 1_555 B SG CYS 30 E CYS 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 B SG CYS 48 E CYS 375 1_555 B SG CYS 101 E CYS 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 B SG CYS 60 E CYS 387 1_555 B SG CYS 194 E CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf7 B SG CYS 149 E CYS 476 1_555 B SG CYS 157 E CYS 484 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 35 A ASN 53 1_555 D C1 NAG . A NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 72 A ASN 90 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 A ND2 ASN 304 A ASN 322 1_555 G C1 NAG . A NAG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 A ND2 ASN 414 A ASN 432 1_555 E C1 NAG . A NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 A ND2 ASN 528 A ASN 546 1_555 F C1 NAG . A NAG 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 B ND2 ASN 12 E ASN 339 1_555 O C1 NAG . E NAG 1701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 B ND2 ASN 39 E ASN 366 1_555 P C1 NAG . E NAG 1702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale8 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? # _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 250 n n C1 O1 NAG sing 251 n n C1 O5 NAG sing 252 n n C1 H1 NAG sing 253 n n C2 C3 NAG sing 254 n n C2 N2 NAG sing 255 n n C2 H2 NAG sing 256 n n C3 C4 NAG sing 257 n n C3 O3 NAG sing 258 n n C3 H3 NAG sing 259 n n C4 C5 NAG sing 260 n n C4 O4 NAG sing 261 n n C4 H4 NAG sing 262 n n C5 C6 NAG sing 263 n n C5 O5 NAG sing 264 n n C5 H5 NAG sing 265 n n C6 O6 NAG sing 266 n n C6 H61 NAG sing 267 n n C6 H62 NAG sing 268 n n C7 C8 NAG sing 269 n n C7 N2 NAG sing 270 n n C7 O7 NAG doub 271 n n C8 H81 NAG sing 272 n n C8 H82 NAG sing 273 n n C8 H83 NAG sing 274 n n N2 HN2 NAG sing 275 n n O1 HO1 NAG sing 276 n n O3 HO3 NAG sing 277 n n O4 HO4 NAG sing 278 n n O6 HO6 NAG sing 279 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 7PKI _atom_sites.fract_transf_matrix[1][1] 0.002928 _atom_sites.fract_transf_matrix[1][2] 0.00169 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003381 _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] 0.014673 _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 D 4 NAG A 1 701 1071 NAG NAG . E 4 NAG A 1 702 1072 NAG NAG . F 4 NAG A 1 703 1073 NAG NAG . G 4 NAG A 1 704 1074 NAG NAG . H 5 SO4 A 1 705 1 SO4 SO4 . I 5 SO4 A 1 706 2 SO4 SO4 . J 5 SO4 A 1 707 3 SO4 SO4 . K 6 TRS A 1 708 1 TRS TRS . L 7 PEG A 1 709 2 PEG PEG . M 7 PEG A 1 710 6 PEG PEG . N 8 ZN A 1 711 1 ZN ZN . O 4 NAG E 1 1701 1701 NAG NAG . P 4 NAG E 1 1702 1702 NAG NAG . Q 5 SO4 E 1 1703 4 SO4 SO4 . R 9 CL E 1 1704 1 CL CL . S 9 CL E 1 1705 2 CL CL . T 7 PEG E 1 1706 1 PEG PEG . U 7 PEG E 1 1707 3 PEG PEG . V 7 PEG E 1 1708 4 PEG PEG . W 10 GOL E 1 1709 1 GOL GOL . X 11 HOH A 1 801 7 HOH HOH . X 11 HOH A 2 802 5 HOH HOH . X 11 HOH A 3 803 1 HOH HOH . X 11 HOH A 4 804 2 HOH HOH . X 11 HOH A 5 805 3 HOH HOH . Y 11 HOH E 1 1801 4 HOH HOH . Y 11 HOH E 2 1802 6 HOH HOH . Y 11 HOH E 3 1803 8 HOH HOH . # 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 . . . O 4 83.611 138.716 4.909 1 77.4 ? C1 NAG 1701 E 1 HETATM 2 C C2 NAG . . . O 4 83.942 140.032 4.207 1 81.13 ? C2 NAG 1701 E 1 HETATM 3 C C3 NAG . . . O 4 84.869 139.781 3.018 1 82.62 ? C3 NAG 1701 E 1 HETATM 4 C C4 NAG . . . O 4 86.091 138.975 3.437 1 83.86 ? C4 NAG 1701 E 1 HETATM 5 C C5 NAG . . . O 4 85.656 137.703 4.155 1 89.63 ? C5 NAG 1701 E 1 HETATM 6 C C6 NAG . . . O 4 86.818 136.907 4.702 1 105.87 ? C6 NAG 1701 E 1 HETATM 7 C C7 NAG . . . O 4 82.566 142.026 3.784 1 80.26 ? C7 NAG 1701 E 1 HETATM 8 C C8 NAG . . . O 4 81.247 142.535 3.285 1 63.61 ? C8 NAG 1701 E 1 HETATM 9 N N2 NAG . . . O 4 82.726 140.699 3.767 1 76.25 ? N2 NAG 1701 E 1 HETATM 10 O O3 NAG . . . O 4 85.28 141.028 2.469 1 86.55 ? O3 NAG 1701 E 1 HETATM 11 O O4 NAG . . . O 4 86.854 138.626 2.288 1 80.7 ? O4 NAG 1701 E 1 HETATM 12 O O5 NAG . . . O 4 84.824 138.043 5.273 1 90.79 ? O5 NAG 1701 E 1 HETATM 13 O O6 NAG . . . O 4 86.438 136.153 5.844 1 91.36 ? O6 NAG 1701 E 1 HETATM 14 O O7 NAG . . . O 4 83.447 142.782 4.185 1 80.04 ? O7 NAG 1701 E 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 14 #