data_3TO4 # _model_server_result.job_id FE2OthNHmDu30JnR9stYFQ _model_server_result.datetime_utc '2024-12-04 23:42:39' _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 3to4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":305}' # _entry.id 3TO4 # _exptl.entry_id 3TO4 _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 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 3TO4 _cell.length_a 59.211 _cell.length_b 82.594 _cell.length_c 238.482 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TO4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 ? 7 G N N ? 7 H N N # _pdbx_entity_branch.entity_id 5 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 5 _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 5 n E NAG 1 E 1 NAG Y 303 NAG 5 n E NAG 2 E 2 NAG Y 304 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 104 A CYS 104 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 C SG CYS 22 C CYS 22 1_555 C SG CYS 89 C CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf5 C SG CYS 136 C CYS 139 1_555 C SG CYS 186 C CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf6 D SG CYS 23 D CYS 23 1_555 D SG CYS 91 D CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf7 D SG CYS 146 D CYS 148 1_555 D SG CYS 211 D CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 G C1 NAG . A NAG 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 H C1 NAG . A NAG 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E 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 396 n n C1 O1 NAG sing 397 n n C1 O5 NAG sing 398 n n C1 H1 NAG sing 399 n n C2 C3 NAG sing 400 n n C2 N2 NAG sing 401 n n C2 H2 NAG sing 402 n n C3 C4 NAG sing 403 n n C3 O3 NAG sing 404 n n C3 H3 NAG sing 405 n n C4 C5 NAG sing 406 n n C4 O4 NAG sing 407 n n C4 H4 NAG sing 408 n n C5 C6 NAG sing 409 n n C5 O5 NAG sing 410 n n C5 H5 NAG sing 411 n n C6 O6 NAG sing 412 n n C6 H61 NAG sing 413 n n C6 H62 NAG sing 414 n n C7 C8 NAG sing 415 n n C7 N2 NAG sing 416 n n C7 O7 NAG doub 417 n n C8 H81 NAG sing 418 n n C8 H82 NAG sing 419 n n C8 H83 NAG sing 420 n n N2 HN2 NAG sing 421 n n O1 HO1 NAG sing 422 n n O3 HO3 NAG sing 423 n n O4 HO4 NAG sing 424 n n O6 HO6 NAG sing 425 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 3TO4 _atom_sites.fract_transf_matrix[1][1] 0.016889 _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] 0.012107 _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] 0.004193 _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 F 6 AGH A 1 303 1 AGH AGH . G 7 NAG A 1 304 301 NAG NAG . H 7 NAG A 1 305 302 NAG NAG . I 8 HOH A 1 308 1 HOH HOH . I 8 HOH A 2 309 2 HOH HOH . I 8 HOH A 3 310 4 HOH HOH . I 8 HOH A 4 311 5 HOH HOH . J 8 HOH C 1 216 3 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 . . . H 7 -0.004 3.42 -75.978 1 61.84 ? C1 NAG 305 A 1 HETATM 2 C C2 NAG . . . H 7 1.528 3.456 -76.024 1 63.68 ? C2 NAG 305 A 1 HETATM 3 C C3 NAG . . . H 7 2.143 3.198 -74.65 1 64.42 ? C3 NAG 305 A 1 HETATM 4 C C4 NAG . . . H 7 1.628 4.242 -73.67 1 65.59 ? C4 NAG 305 A 1 HETATM 5 C C5 NAG . . . H 7 0.099 4.117 -73.651 1 63.25 ? C5 NAG 305 A 1 HETATM 6 C C6 NAG . . . H 7 -0.555 5.141 -72.734 1 64.47 ? C6 NAG 305 A 1 HETATM 7 C C7 NAG . . . H 7 2.358 2.861 -78.222 1 64.52 ? C7 NAG 305 A 1 HETATM 8 C C8 NAG . . . H 7 2.911 1.772 -79.085 1 64.43 ? C8 NAG 305 A 1 HETATM 9 N N2 NAG . . . H 7 2.063 2.508 -76.975 1 63.45 ? N2 NAG 305 A 1 HETATM 10 O O3 NAG . . . H 7 3.545 3.25 -74.716 1 66.43 ? O3 NAG 305 A 1 HETATM 11 O O4 NAG . . . H 7 2.225 4.077 -72.394 1 66.22 ? O4 NAG 305 A 1 HETATM 12 O O5 NAG . . . H 7 -0.441 4.303 -74.954 1 62.45 ? O5 NAG 305 A 1 HETATM 13 O O6 NAG . . . H 7 -1.883 4.72 -72.511 1 63.18 ? O6 NAG 305 A 1 HETATM 14 O O7 NAG . . . H 7 2.19 3.993 -78.675 1 65.55 ? O7 NAG 305 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 14 #