data_5SVM # _model_server_result.job_id XVJu5jQ0XQ7rSvJJBQm6Jg _model_server_result.datetime_utc '2024-11-05 21:17:38' _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 5svm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":403}' # _entry.id 5SVM # _exptl.entry_id 5SVM _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 6 _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 5SVM _cell.length_a 172.64 _cell.length_b 172.64 _cell.length_c 172.64 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,P 1 1,2,4 B,J,K,L,M,N,O,Q 2 1,3,5 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 6_555 z+1/2,-x+1/2,-y 0 0 1 -1 0 0 0 -1 0 86.32 86.32 0 4 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 5 'crystal symmetry operation' 12_554 -y+1/2,-z,x-1/2 0 -1 0 0 0 -1 1 0 0 86.32 0 -86.32 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N N ? 2 E N N ? 2 K N N ? 2 L N N ? 2 M 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 106 B CYS 107 1_555 B SG CYS 152 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 B SG CYS 115 B CYS 116 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 121 B CYS 122 1_555 B SG CYS 146 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 202 B CYS 203 1_555 B SG CYS 212 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf10 B SG CYS 246 B CYS 247 1_555 B SG CYS 255 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 193 A ASN 194 1_555 D C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 289 A ASN 290 1_555 E C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 B ND2 ASN 169 B ASN 170 1_555 K C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 B ND2 ASN 193 B ASN 194 1_555 L C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale6 B ND2 ASN 289 B ASN 290 1_555 M C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 F OAI 6AT . A 6AT 404 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc2 F OAC 6AT . A 6AT 404 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.011 ? metalc ? metalc3 G NA NA . A NA 405 1_555 P O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc4 G NA NA . A NA 405 1_555 P O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? metalc ? metalc5 G NA NA . A NA 405 1_555 P O HOH . A HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc6 G NA NA . A NA 405 1_555 P O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc7 B OD2 ASP 157 B ASP 158 1_555 N NA NA . B NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc8 N NA NA . B NA 405 1_555 Q O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.002 ? metalc ? metalc9 N NA NA . B NA 405 1_555 Q O HOH . B HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? # _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 348 n n C1 O1 NAG sing 349 n n C1 O5 NAG sing 350 n n C1 H1 NAG sing 351 n n C2 C3 NAG sing 352 n n C2 N2 NAG sing 353 n n C2 H2 NAG sing 354 n n C3 C4 NAG sing 355 n n C3 O3 NAG sing 356 n n C3 H3 NAG sing 357 n n C4 C5 NAG sing 358 n n C4 O4 NAG sing 359 n n C4 H4 NAG sing 360 n n C5 C6 NAG sing 361 n n C5 O5 NAG sing 362 n n C5 H5 NAG sing 363 n n C6 O6 NAG sing 364 n n C6 H61 NAG sing 365 n n C6 H62 NAG sing 366 n n C7 C8 NAG sing 367 n n C7 N2 NAG sing 368 n n C7 O7 NAG doub 369 n n C8 H81 NAG sing 370 n n C8 H82 NAG sing 371 n n C8 H83 NAG sing 372 n n N2 HN2 NAG sing 373 n n O1 HO1 NAG sing 374 n n O3 HO3 NAG sing 375 n n O4 HO4 NAG sing 376 n n O6 HO6 NAG sing 377 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 5SVM _atom_sites.fract_transf_matrix[1][1] 0.005792 _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] 0.005792 _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] 0.005792 _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 2 NAG A 1 401 500 NAG NAG . D 2 NAG A 1 402 501 NAG NAG . E 2 NAG A 1 403 502 NAG NAG . F 3 6AT A 1 404 1 6AT LIG . G 4 NA A 1 405 4 NA NA . H 5 TRS A 1 406 1 TRS TRS . I 6 EDO A 1 407 1 EDO EDO . J 7 ATP B 1 401 402 ATP ATP . K 2 NAG B 1 402 500 NAG NAG . L 2 NAG B 1 403 501 NAG NAG . M 2 NAG B 1 404 502 NAG NAG . N 4 NA B 1 405 3 NA NA . O 6 EDO B 1 406 2 EDO EDO . P 8 HOH A 1 501 20 HOH HOH . P 8 HOH A 2 502 40 HOH HOH . P 8 HOH A 3 503 52 HOH HOH . P 8 HOH A 4 504 3 HOH HOH . P 8 HOH A 5 505 44 HOH HOH . P 8 HOH A 6 506 6 HOH HOH . P 8 HOH A 7 507 1 HOH HOH . P 8 HOH A 8 508 5 HOH HOH . P 8 HOH A 9 509 4 HOH HOH . P 8 HOH A 10 510 11 HOH HOH . P 8 HOH A 11 511 43 HOH HOH . P 8 HOH A 12 512 14 HOH HOH . P 8 HOH A 13 513 26 HOH HOH . P 8 HOH A 14 514 49 HOH HOH . P 8 HOH A 15 515 54 HOH HOH . P 8 HOH A 16 516 15 HOH HOH . P 8 HOH A 17 517 45 HOH HOH . P 8 HOH A 18 518 42 HOH HOH . P 8 HOH A 19 519 2 HOH HOH . Q 8 HOH B 1 501 29 HOH HOH . Q 8 HOH B 2 502 22 HOH HOH . Q 8 HOH B 3 503 48 HOH HOH . Q 8 HOH B 4 504 37 HOH HOH . Q 8 HOH B 5 505 36 HOH HOH . Q 8 HOH B 6 506 23 HOH HOH . Q 8 HOH B 7 507 33 HOH HOH . Q 8 HOH B 8 508 51 HOH HOH . Q 8 HOH B 9 509 19 HOH HOH . Q 8 HOH B 10 510 50 HOH HOH . Q 8 HOH B 11 511 28 HOH HOH . Q 8 HOH B 12 512 32 HOH HOH . Q 8 HOH B 13 513 16 HOH HOH . Q 8 HOH B 14 514 35 HOH HOH . Q 8 HOH B 15 515 53 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 . . . L 2 59.55 -1.099 -39.817 1 85.96 ? C1 NAG 403 B 1 HETATM 2 C C2 NAG . . . L 2 58.401 -2.039 -39.424 1 81.48 ? C2 NAG 403 B 1 HETATM 3 C C3 NAG . . . L 2 58.383 -2.186 -37.905 1 86.77 ? C3 NAG 403 B 1 HETATM 4 C C4 NAG . . . L 2 59.741 -2.69 -37.425 1 82.71 ? C4 NAG 403 B 1 HETATM 5 C C5 NAG . . . L 2 60.837 -1.717 -37.865 1 78.4 ? C5 NAG 403 B 1 HETATM 6 C C6 NAG . . . L 2 62.209 -2.232 -37.419 1 87.72 ? C6 NAG 403 B 1 HETATM 7 C C7 NAG . . . L 2 55.998 -2.441 -39.753 1 104.37 ? C7 NAG 403 B 1 HETATM 8 C C8 NAG . . . L 2 54.599 -2.022 -40.209 1 84.02 ? C8 NAG 403 B 1 HETATM 9 N N2 NAG . . . L 2 57.067 -1.619 -39.882 1 95.1 ? N2 NAG 403 B 1 HETATM 10 O O3 NAG . . . L 2 57.337 -3.077 -37.492 1 103.2 ? O3 NAG 403 B 1 HETATM 11 O O4 NAG . . . L 2 59.737 -2.851 -35.998 1 96.3 ? O4 NAG 403 B 1 HETATM 12 O O5 NAG . . . L 2 60.807 -1.542 -39.291 1 81.28 ? O5 NAG 403 B 1 HETATM 13 O O6 NAG . . . L 2 62.228 -2.438 -35.999 1 126.22 ? O6 NAG 403 B 1 HETATM 14 O O7 NAG . . . L 2 56.172 -3.548 -39.256 1 117.52 ? O7 NAG 403 B 1 HETATM 15 H H1 NAG . . . L 2 59.324 -0.095 -39.43 1 103.15 ? H1 NAG 403 B 1 HETATM 16 H H2 NAG . . . L 2 58.627 -3.025 -39.861 1 97.77 ? H2 NAG 403 B 1 HETATM 17 H H3 NAG . . . L 2 58.206 -1.19 -37.472 1 104.13 ? H3 NAG 403 B 1 HETATM 18 H H4 NAG . . . L 2 59.938 -3.672 -37.885 1 99.26 ? H4 NAG 403 B 1 HETATM 19 H H5 NAG . . . L 2 60.665 -0.736 -37.389 1 94.08 ? H5 NAG 403 B 1 HETATM 20 H H61 NAG . . . L 2 62.981 -1.509 -37.692 1 105.26 ? H61 NAG 403 B 1 HETATM 21 H H62 NAG . . . L 2 62.444 -3.18 -37.912 1 105.26 ? H62 NAG 403 B 1 HETATM 22 H H81 NAG . . . L 2 53.935 -2.05 -39.382 1 100.82 ? H81 NAG 403 B 1 HETATM 23 H H82 NAG . . . L 2 54.249 -2.702 -40.944 1 100.82 ? H82 NAG 403 B 1 HETATM 24 H H83 NAG . . . L 2 54.554 -1.043 -40.626 1 100.82 ? H83 NAG 403 B 1 HETATM 25 H HN2 NAG . . . L 2 56.939 -0.696 -40.294 1 114.12 ? HN2 NAG 403 B 1 HETATM 26 H HO3 NAG . . . L 2 57.097 -2.888 -36.574 1 123.84 ? HO3 NAG 403 B 1 HETATM 27 H HO4 NAG . . . L 2 59.602 -3.783 -35.779 1 115.56 ? HO4 NAG 403 B 1 HETATM 28 H HO6 NAG . . . L 2 62.442 -1.605 -35.556 1 151.47 ? HO6 NAG 403 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #