data_5SVS # _model_server_result.job_id IepAn2CnQwMhU1nTq9vPHA _model_server_result.datetime_utc '2024-11-30 07:56:02' _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 5svs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5SVS # _exptl.entry_id 5SVS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 2 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 5SVS _cell.length_a 120.2 _cell.length_b 120.2 _cell.length_c 236.24 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVS _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D 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 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 B C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 A ND2 ASN 193 A ASN 194 1_555 C C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale3 A ND2 ASN 289 A ASN 290 1_555 D C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? # _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 246 n n C1 O1 NAG sing 247 n n C1 O5 NAG sing 248 n n C1 H1 NAG sing 249 n n C2 C3 NAG sing 250 n n C2 N2 NAG sing 251 n n C2 H2 NAG sing 252 n n C3 C4 NAG sing 253 n n C3 O3 NAG sing 254 n n C3 H3 NAG sing 255 n n C4 C5 NAG sing 256 n n C4 O4 NAG sing 257 n n C4 H4 NAG sing 258 n n C5 C6 NAG sing 259 n n C5 O5 NAG sing 260 n n C5 H5 NAG sing 261 n n C6 O6 NAG sing 262 n n C6 H61 NAG sing 263 n n C6 H62 NAG sing 264 n n C7 C8 NAG sing 265 n n C7 N2 NAG sing 266 n n C7 O7 NAG doub 267 n n C8 H81 NAG sing 268 n n C8 H82 NAG sing 269 n n C8 H83 NAG sing 270 n n N2 HN2 NAG sing 271 n n O1 HO1 NAG sing 272 n n O3 HO3 NAG sing 273 n n O4 HO4 NAG sing 274 n n O6 HO6 NAG sing 275 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 5SVS _atom_sites.fract_transf_matrix[1][1] 0.008319 _atom_sites.fract_transf_matrix[1][2] 0.004803 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009606 _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] 0.004233 _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 B 2 NAG A 1 401 500 NAG NAG . C 2 NAG A 1 402 501 NAG NAG . D 2 NAG A 1 403 502 NAG NAG . E 3 MG A 1 404 1 MG MG . F 4 NA A 1 405 1 NA NA . G 5 PG4 A 1 406 1 PG4 PG4 . H 6 EDO A 1 407 1 EDO EDO . I 7 HOH A 1 501 12 HOH HOH . I 7 HOH A 2 502 3 HOH HOH . I 7 HOH A 3 503 19 HOH HOH . I 7 HOH A 4 504 29 HOH HOH . I 7 HOH A 5 505 9 HOH HOH . I 7 HOH A 6 506 13 HOH HOH . I 7 HOH A 7 507 18 HOH HOH . I 7 HOH A 8 508 26 HOH HOH . I 7 HOH A 9 509 16 HOH HOH . I 7 HOH A 10 510 11 HOH HOH . I 7 HOH A 11 511 1 HOH HOH . I 7 HOH A 12 512 24 HOH HOH . I 7 HOH A 13 513 22 HOH HOH . I 7 HOH A 14 514 30 HOH HOH . I 7 HOH A 15 515 7 HOH HOH . I 7 HOH A 16 516 2 HOH HOH . I 7 HOH A 17 517 31 HOH HOH . I 7 HOH A 18 518 27 HOH HOH . I 7 HOH A 19 519 4 HOH HOH . I 7 HOH A 20 520 14 HOH HOH . I 7 HOH A 21 521 20 HOH HOH . I 7 HOH A 22 522 8 HOH HOH . I 7 HOH A 23 523 15 HOH HOH . I 7 HOH A 24 524 17 HOH HOH . I 7 HOH A 25 525 6 HOH HOH . I 7 HOH A 26 526 5 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 . . . B 2 -15.416 25.104 -34.13 1 237.02 ? C1 NAG 401 A 1 HETATM 2 C C2 NAG . . . B 2 -16.603 24.912 -33.185 1 229.14 ? C2 NAG 401 A 1 HETATM 3 C C3 NAG . . . B 2 -17.499 26.15 -33.195 1 234.09 ? C3 NAG 401 A 1 HETATM 4 C C4 NAG . . . B 2 -16.682 27.397 -32.891 1 255.1 ? C4 NAG 401 A 1 HETATM 5 C C5 NAG . . . B 2 -15.522 27.499 -33.871 1 264.53 ? C5 NAG 401 A 1 HETATM 6 C C6 NAG . . . B 2 -14.585 28.643 -33.568 1 246.97 ? C6 NAG 401 A 1 HETATM 7 C C7 NAG . . . B 2 -17.768 22.819 -32.647 1 206.69 ? C7 NAG 401 A 1 HETATM 8 C C8 NAG . . . B 2 -18.554 21.665 -33.189 1 197.5 ? C8 NAG 401 A 1 HETATM 9 N N2 NAG . . . B 2 -17.368 23.728 -33.542 1 221.72 ? N2 NAG 401 A 1 HETATM 10 O O3 NAG . . . B 2 -18.527 25.994 -32.223 1 236.79 ? O3 NAG 401 A 1 HETATM 11 O O4 NAG . . . B 2 -17.497 28.558 -33.005 1 247.45 ? O4 NAG 401 A 1 HETATM 12 O O5 NAG . . . B 2 -14.73 26.306 -33.804 1 273.98 ? O5 NAG 401 A 1 HETATM 13 O O6 NAG . . . B 2 -13.632 28.813 -34.609 1 259.45 ? O6 NAG 401 A 1 HETATM 14 O O7 NAG . . . B 2 -17.503 22.921 -31.453 1 220.3 ? O7 NAG 401 A 1 HETATM 15 H H1 NAG . . . B 2 -15.741 25.158 -35.049 1 284.42 ? H1 NAG 401 A 1 HETATM 16 H H2 NAG . . . B 2 -16.257 24.797 -32.28 1 274.97 ? H2 NAG 401 A 1 HETATM 17 H H3 NAG . . . B 2 -17.905 26.242 -34.077 1 280.91 ? H3 NAG 401 A 1 HETATM 18 H H4 NAG . . . B 2 -16.331 27.339 -31.982 1 306.12 ? H4 NAG 401 A 1 HETATM 19 H H5 NAG . . . B 2 -15.873 27.602 -34.776 1 317.43 ? H5 NAG 401 A 1 HETATM 20 H H61 NAG . . . B 2 -14.116 28.46 -32.731 1 296.37 ? H61 NAG 401 A 1 HETATM 21 H H62 NAG . . . B 2 -15.103 29.465 -33.471 1 296.37 ? H62 NAG 401 A 1 HETATM 22 H H81 NAG . . . B 2 -18.014 21.182 -33.843 1 237 ? H81 NAG 401 A 1 HETATM 23 H H82 NAG . . . B 2 -18.796 21.064 -32.459 1 237 ? H82 NAG 401 A 1 HETATM 24 H H83 NAG . . . B 2 -19.365 21.997 -33.619 1 237 ? H83 NAG 401 A 1 HETATM 25 H HN2 NAG . . . B 2 -17.594 23.605 -34.417 1 266.06 ? HN2 NAG 401 A 1 HETATM 26 H HO3 NAG . . . B 2 -18.166 25.967 -31.412 1 284.15 ? HO3 NAG 401 A 1 HETATM 27 H HO4 NAG . . . B 2 -17.135 29.118 -33.591 1 296.94 ? HO4 NAG 401 A 1 HETATM 28 H HO6 NAG . . . B 2 -12.917 29.231 -34.29 1 311.34 ? HO6 NAG 401 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 1376 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 28 #