data_3ZPB # _model_server_result.job_id MY2xlhZUU8rcu1MW6X4fnw _model_server_result.datetime_utc '2024-11-23 22:36:55' _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 3zpb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":421}' # _entry.id 3ZPB # _exptl.entry_id 3ZPB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 1 _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 3ZPB _cell.length_a 101.108 _cell.length_b 101.108 _cell.length_c 448.315 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3ZPB _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -50.554 87.562097 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -101.108 0 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 . O4 HO4 . sing 2 ? 3 3 2 SIA GAL C2 O2 . 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 C NAG 1 A 1 NAG E 1003 NAG 3 n C GAL 2 A 2 GAL E 1002 GAL 3 n C SIA 3 A 3 SIA E 1001 SIA # 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 20 E CYS 8 1_555 B SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? disulf ? disulf2 A SG CYS 58 E CYS 46 1_555 A SG CYS 290 E CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf3 A SG CYS 71 E CYS 59 1_555 A SG CYS 83 E CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 106 E CYS 94 1_555 A SG CYS 151 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.703 ? disulf ? disulf5 A SG CYS 294 E CYS 282 1_555 A SG CYS 318 E CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? disulf ? disulf6 B SG CYS 144 F CYS 144 1_555 B SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale1 A ND2 ASN 181 E ASN 169 1_555 D C1 NAG . F NAG 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.368 ? covale ? covale2 C O4 NAG . A NAG 1 1_555 C C1 GAL . A GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 C O3 GAL . A GAL 2 1_555 C C2 SIA . A SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? # _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 3ZPB _atom_sites.fract_transf_matrix[1][1] 0.00989 _atom_sites.fract_transf_matrix[1][2] 0.00571 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01142 _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] 0.002231 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id D _pdbx_nonpoly_scheme.entity_id 4 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id F _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 421 _pdbx_nonpoly_scheme.auth_seq_num 421 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . D 4 -45.809 -0.415 -13.953 1 110.37 ? C1 NAG 421 F 1 HETATM 2 C C2 NAG . . . D 4 -47.251 -0.768 -14.283 1 110.89 ? C2 NAG 421 F 1 HETATM 3 C C3 NAG . . . D 4 -47.716 -1.938 -13.439 1 110.56 ? C3 NAG 421 F 1 HETATM 4 C C4 NAG . . . D 4 -46.804 -3.102 -13.738 1 110.49 ? C4 NAG 421 F 1 HETATM 5 C C5 NAG . . . D 4 -45.386 -2.69 -13.381 1 110.52 ? C5 NAG 421 F 1 HETATM 6 C C6 NAG . . . D 4 -44.4 -3.83 -13.605 1 110.99 ? C6 NAG 421 F 1 HETATM 7 C C7 NAG . . . D 4 -48.456 1.135 -15.097 1 111.8 ? C7 NAG 421 F 1 HETATM 8 C C8 NAG . . . D 4 -49.428 2.235 -14.808 1 111.27 ? C8 NAG 421 F 1 HETATM 9 N N2 NAG . . . D 4 -48.114 0.368 -14.073 1 111.83 ? N2 NAG 421 F 1 HETATM 10 O O3 NAG . . . D 4 -49.057 -2.291 -13.771 1 110.46 ? O3 NAG 421 F 1 HETATM 11 O O4 NAG . . . D 4 -47.227 -4.231 -12.972 1 111.01 ? O4 NAG 421 F 1 HETATM 12 O O5 NAG . . . D 4 -44.998 -1.565 -14.17 1 110.39 ? O5 NAG 421 F 1 HETATM 13 O O6 NAG . . . D 4 -44.744 -4.557 -14.789 1 111.74 ? O6 NAG 421 F 1 HETATM 14 O O7 NAG . . . D 4 -48 0.949 -16.206 1 111.77 ? O7 NAG 421 F 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #