data_3ZYI # _model_server_result.job_id pGH0ylj6ZDdifAE3FXc6Jg _model_server_result.datetime_utc '2024-11-04 22:45:17' _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 3zyi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1348}' # _entry.id 3ZYI # _exptl.entry_id 3ZYI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _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 3ZYI _cell.length_a 75.42 _cell.length_b 153.39 _cell.length_c 158.73 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZYI _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 2 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 _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 ? 3 C N N ? 3 F N N # 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 46 A CYS 46 1_555 A SG CYS 52 A CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? disulf ? disulf2 A SG CYS 50 A CYS 50 1_555 A SG CYS 61 A CYS 61 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 304 A CYS 304 1_555 A SG CYS 329 A CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 A SG CYS 306 A CYS 306 1_555 A SG CYS 350 A CYS 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 374 A CYS 374 1_555 A SG CYS 424 A CYS 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 22 B CYS 22 1_555 B SG CYS 39 B CYS 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 B SG CYS 61 B CYS 61 1_555 B SG CYS 81 B CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 B SG CYS 69 B CYS 69 1_555 B SG CYS 77 B CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf9 B SG CYS 171 B CYS 171 1_555 B SG CYS 195 B CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf10 B SG CYS 287 B CYS 287 1_555 B SG CYS 296 B CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf11 B SG CYS 289 B CYS 289 1_555 B SG CYS 305 B CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf12 B SG CYS 307 B CYS 307 1_555 B SG CYS 316 B CYS 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 B SG CYS 319 B CYS 319 1_555 B SG CYS 344 B CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A ND2 ASN 363 A ASN 363 1_555 C C1 NAG . A NAG 1442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale2 B ND2 ASN 122 B ASN 122 1_555 F C1 NAG . B NAG 1348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.482 ? metalc ? metalc1 B O LEU 94 B LEU 94 1_555 G CA CA . B CA 1349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc2 B OD1 ASP 97 B ASP 97 1_555 G CA CA . B CA 1349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc3 B OE2 GLU 99 B GLU 99 1_555 G CA CA . B CA 1349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc4 B O THR 105 B THR 105 1_555 G CA CA . B CA 1349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc5 B OG1 THR 105 B THR 105 1_555 G CA CA . B CA 1349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? metalc ? metalc6 B O SER 279 B SER 279 1_555 G CA CA . B CA 1349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 3ZYI _atom_sites.fract_transf_matrix[1][1] 0.013259 _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] 0.006519 _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] 0.0063 _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 C 3 NAG A 1 1442 1442 NAG NAG . D 4 PO4 A 1 1443 1443 PO4 PO4 . E 4 PO4 A 1 1444 1444 PO4 PO4 . F 3 NAG B 1 1348 1348 NAG NAG . G 5 CA B 1 1349 1349 CA CA . # 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 . . . F 3 -2.993 30.185 37.537 1 78.88 ? C1 NAG 1348 B 1 HETATM 2 C C2 NAG . . . F 3 -4.303 30.18 38.339 1 78.65 ? C2 NAG 1348 B 1 HETATM 3 C C3 NAG . . . F 3 -4.347 31.418 39.229 1 78.23 ? C3 NAG 1348 B 1 HETATM 4 C C4 NAG . . . F 3 -3.128 31.377 40.147 1 80.03 ? C4 NAG 1348 B 1 HETATM 5 C C5 NAG . . . F 3 -1.874 31.367 39.263 1 80.61 ? C5 NAG 1348 B 1 HETATM 6 C C6 NAG . . . F 3 -0.649 31.349 40.178 1 82.24 ? C6 NAG 1348 B 1 HETATM 7 C C7 NAG . . . F 3 -6.158 29.075 37.171 1 79.51 ? C7 NAG 1348 B 1 HETATM 8 C C8 NAG . . . F 3 -7.338 29.144 36.241 1 79.33 ? C8 NAG 1348 B 1 HETATM 9 N N2 NAG . . . F 3 -5.457 30.197 37.436 1 79.01 ? N2 NAG 1348 B 1 HETATM 10 O O3 NAG . . . F 3 -5.549 31.434 39.999 1 76.89 ? O3 NAG 1348 B 1 HETATM 11 O O4 NAG . . . F 3 -3.128 32.532 40.989 1 81.08 ? O4 NAG 1348 B 1 HETATM 12 O O5 NAG . . . F 3 -1.86 30.188 38.425 1 79.59 ? O5 NAG 1348 B 1 HETATM 13 O O6 NAG . . . F 3 0.532 31.373 39.379 1 83.69 ? O6 NAG 1348 B 1 HETATM 14 O O7 NAG . . . F 3 -5.841 28.015 37.674 1 80.24 ? O7 NAG 1348 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #