data_3LZF # _model_server_result.job_id t18n5g8oIX7058drBLLUAQ _model_server_result.datetime_utc '2024-11-28 09:28:55' _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 3lzf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":401}' # _entry.id 3LZF # _exptl.entry_id 3LZF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _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 3LZF _cell.length_a 161.745 _cell.length_b 161.745 _cell.length_c 143.473 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LZF _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 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 ? dodecameric 12 author_defined_assembly 1 PISA hexameric 6 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # 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,F,G,H 1 1,2,3 A,B,E,F,G,H 2 1,2,3 C,D 3 1 # 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_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 80.8725 -140.075279 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 161.745 0 0 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 6 4 3 MAN BMA 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 5 n E NAG 1 C 1 NAG A 501 NAG 5 n E NAG 2 C 2 NAG A 502 NAG 6 n F NAG 1 D 1 NAG A 601 NAG 6 n F NAG 2 D 2 NAG A 602 NAG 6 n F BMA 3 D 3 BMA A 603 BMA 6 n F MAN 4 D 4 MAN A 604 MAN 5 n G NAG 1 E 1 NAG A 701 NAG 5 n G NAG 2 E 2 NAG A 702 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 8 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 46 A CYS 52 1_555 A SG CYS 279 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? disulf ? disulf3 A SG CYS 59 A CYS 64 1_555 A SG CYS 71 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? disulf ? disulf4 A SG CYS 94 A CYS 97 1_555 A SG CYS 140 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? disulf ? disulf5 A SG CYS 283 A CYS 281 1_555 A SG CYS 307 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 C SG CYS 22 H CYS 22 1_555 C SG CYS 100 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf8 C SG CYS 154 H CYS 142 1_555 C SG CYS 210 H CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf9 D SG CYS 22 L CYS 23 1_555 D SG CYS 89 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf10 D SG CYS 139 L CYS 134 1_555 D SG CYS 198 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A ND2 ASN 15 A ASN 21 1_555 H C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 A ND2 ASN 27 A ASN 33 1_555 E C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale3 A ND2 ASN 91 A ASN 95 1_555 F C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale4 A ND2 ASN 291 A ASN 289 1_555 G C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale5 E O4 NAG . C NAG 1 1_555 E C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 F O4 NAG . D NAG 1 1_555 F C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 F O4 NAG . D NAG 2 1_555 F C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale8 F O3 BMA . D BMA 3 1_555 F C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale9 G O4 NAG . E NAG 1 1_555 G C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 3LZF _atom_sites.fract_transf_matrix[1][1] 0.006183 _atom_sites.fract_transf_matrix[1][2] 0.00357 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007139 _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] 0.00697 _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 H _pdbx_nonpoly_scheme.entity_id 7 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 401 _pdbx_nonpoly_scheme.auth_seq_num 401 _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 . . . H 7 53.598 -29.911 -3.165 1 119.87 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . H 7 52.877 -28.551 -3.086 1 127 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . H 7 51.499 -28.739 -2.436 1 127.02 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . H 7 50.729 -29.688 -3.357 1 127.13 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . H 7 51.46 -31.047 -3.329 1 126.05 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . H 7 50.724 -32.144 -4.119 1 126 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . H 7 54.449 -26.624 -3.065 1 132.59 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . H 7 55.251 -25.67 -2.209 1 132.04 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . H 7 53.715 -27.551 -2.414 1 130.24 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . H 7 50.809 -27.522 -2.213 1 127.37 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . H 7 49.354 -29.773 -3.009 1 127.98 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . H 7 52.801 -30.905 -3.809 1 123.25 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . H 7 51.568 -33.262 -4.335 1 125.84 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . H 7 54.474 -26.506 -4.299 1 133.89 ? O7 NAG 401 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 14 #