data_1VBM # _model_server_result.job_id r9e0Tgyepa6rzcDrI3H9oQ _model_server_result.datetime_utc '2024-11-29 00:18:15' _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 1vbm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":3002}' # _entry.id 1VBM # _exptl.entry_id 1VBM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 509.493 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE" _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 120 _cell.entry_id 1VBM _cell.length_a 83.189 _cell.length_b 83.189 _cell.length_c 182.424 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VBM _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 ? 3 E N N ? 3 H N N # _chem_comp.formula 'C19 H23 N7 O8 S' _chem_comp.formula_weight 509.493 _chem_comp.id YSA _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms TYROSYLADENYLATE # 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 CD1 CE1 YSA doub 380 n y CD1 CG YSA sing 381 n y CD1 HD1 YSA sing 382 n n CE1 CZ YSA sing 383 n y CE1 HE1 YSA sing 384 n n CZ OH YSA sing 385 n n CZ CE2 YSA doub 386 n y OH HOH YSA sing 387 n n CE2 CD2 YSA sing 388 n y CE2 HE2 YSA sing 389 n n CD2 CG YSA doub 390 n y CD2 HD2 YSA sing 391 n n CG CB YSA sing 392 n n CB CA YSA sing 393 n n CB HB1 YSA sing 394 n n CB HB2 YSA sing 395 n n CA N YSA sing 396 n n CA C YSA sing 397 n n CA HA YSA sing 398 n n N HN1 YSA sing 399 n n N HN2 YSA sing 400 n n C O YSA doub 401 n n C NAT YSA sing 402 n n NAT SBI YSA sing 403 n n NAT HAT YSA sing 404 n n SBI OAD YSA doub 405 n n SBI OAE YSA doub 406 n n SBI O5' YSA sing 407 n n O5' C5' YSA sing 408 n n C5' C4' YSA sing 409 n n C5' "H5'1" YSA sing 410 n n C5' "H5'2" YSA sing 411 n n C4' O4' YSA sing 412 n n C4' C3' YSA sing 413 n n C4' H4' YSA sing 414 n n O4' C1' YSA sing 415 n n C3' O3' YSA sing 416 n n C3' C2' YSA sing 417 n n C3' H3' YSA sing 418 n n O3' H3 YSA sing 419 n n C2' O2' YSA sing 420 n n C2' C1' YSA sing 421 n n C2' H2' YSA sing 422 n n O2' H1 YSA sing 423 n n C1' N9 YSA sing 424 n n C1' H1' YSA sing 425 n n N9 C8 YSA sing 426 n y N9 C4 YSA sing 427 n y C8 N7 YSA doub 428 n y C8 H8 YSA sing 429 n n N7 C5 YSA sing 430 n y C5 C4 YSA doub 431 n y C5 C6 YSA sing 432 n y C4 N3 YSA sing 433 n y N3 C2 YSA doub 434 n y C2 N1 YSA sing 435 n y C2 H2 YSA sing 436 n n N1 C6 YSA doub 437 n y C6 N6 YSA sing 438 n n N6 HN61 YSA sing 439 n n N6 HN62 YSA sing 440 n n # _atom_sites.entry_id 1VBM _atom_sites.fract_transf_matrix[1][1] 0.012021 _atom_sites.fract_transf_matrix[1][2] 0.00694 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01388 _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] 0.005482 _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 SO4 A 1 2003 2003 SO4 SUL . D 2 SO4 A 1 2004 2004 SO4 SUL . E 3 YSA A 1 3001 3001 YSA YSA . F 2 SO4 B 1 2001 2001 SO4 SUL . G 2 SO4 B 1 2002 2002 SO4 SUL . H 3 YSA B 1 3002 3002 YSA YSA . I 4 HOH A 1 3002 1 HOH TIP . I 4 HOH A 2 3003 3 HOH TIP . I 4 HOH A 3 3004 4 HOH TIP . I 4 HOH A 4 3005 5 HOH TIP . I 4 HOH A 5 3006 7 HOH TIP . I 4 HOH A 6 3007 8 HOH TIP . I 4 HOH A 7 3008 10 HOH TIP . I 4 HOH A 8 3009 11 HOH TIP . I 4 HOH A 9 3010 14 HOH TIP . I 4 HOH A 10 3011 15 HOH TIP . I 4 HOH A 11 3012 16 HOH TIP . I 4 HOH A 12 3013 27 HOH TIP . I 4 HOH A 13 3014 31 HOH TIP . I 4 HOH A 14 3015 32 HOH TIP . I 4 HOH A 15 3016 33 HOH TIP . I 4 HOH A 16 3017 34 HOH TIP . I 4 HOH A 17 3018 35 HOH TIP . I 4 HOH A 18 3019 36 HOH TIP . I 4 HOH A 19 3020 37 HOH TIP . I 4 HOH A 20 3021 38 HOH TIP . I 4 HOH A 21 3022 39 HOH TIP . I 4 HOH A 22 3023 42 HOH TIP . I 4 HOH A 23 3024 50 HOH TIP . I 4 HOH A 24 3025 51 HOH TIP . I 4 HOH A 25 3026 54 HOH TIP . I 4 HOH A 26 3027 55 HOH TIP . I 4 HOH A 27 3028 58 HOH TIP . I 4 HOH A 28 3029 60 HOH TIP . I 4 HOH A 29 3030 61 HOH TIP . I 4 HOH A 30 3031 65 HOH TIP . I 4 HOH A 31 3032 67 HOH TIP . I 4 HOH A 32 3033 72 HOH TIP . I 4 HOH A 33 3034 73 HOH TIP . I 4 HOH A 34 3035 76 HOH TIP . I 4 HOH A 35 3036 77 HOH TIP . I 4 HOH A 36 3037 78 HOH TIP . I 4 HOH A 37 3038 81 HOH TIP . I 4 HOH A 38 3039 82 HOH TIP . I 4 HOH A 39 3040 85 HOH TIP . I 4 HOH A 40 3041 87 HOH TIP . I 4 HOH A 41 3042 88 HOH TIP . J 4 HOH B 1 3003 2 HOH TIP . J 4 HOH B 2 3004 6 HOH TIP . J 4 HOH B 3 3005 9 HOH TIP . J 4 HOH B 4 3006 12 HOH TIP . J 4 HOH B 5 3007 13 HOH TIP . J 4 HOH B 6 3008 17 HOH TIP . J 4 HOH B 7 3009 18 HOH TIP . J 4 HOH B 8 3010 19 HOH TIP . J 4 HOH B 9 3011 20 HOH TIP . J 4 HOH B 10 3012 21 HOH TIP . J 4 HOH B 11 3013 22 HOH TIP . J 4 HOH B 12 3014 23 HOH TIP . J 4 HOH B 13 3015 24 HOH TIP . J 4 HOH B 14 3016 25 HOH TIP . J 4 HOH B 15 3017 26 HOH TIP . J 4 HOH B 16 3018 28 HOH TIP . J 4 HOH B 17 3019 29 HOH TIP . J 4 HOH B 18 3020 30 HOH TIP . J 4 HOH B 19 3021 40 HOH TIP . J 4 HOH B 20 3022 41 HOH TIP . J 4 HOH B 21 3023 43 HOH TIP . J 4 HOH B 22 3024 44 HOH TIP . J 4 HOH B 23 3025 45 HOH TIP . J 4 HOH B 24 3026 46 HOH TIP . J 4 HOH B 25 3027 47 HOH TIP . J 4 HOH B 26 3028 48 HOH TIP . J 4 HOH B 27 3029 49 HOH TIP . J 4 HOH B 28 3030 52 HOH TIP . J 4 HOH B 29 3031 53 HOH TIP . J 4 HOH B 30 3032 56 HOH TIP . J 4 HOH B 31 3033 57 HOH TIP . J 4 HOH B 32 3034 59 HOH TIP . J 4 HOH B 33 3035 62 HOH TIP . J 4 HOH B 34 3036 63 HOH TIP . J 4 HOH B 35 3037 64 HOH TIP . J 4 HOH B 36 3038 66 HOH TIP . J 4 HOH B 37 3039 68 HOH TIP . J 4 HOH B 38 3040 69 HOH TIP . J 4 HOH B 39 3041 70 HOH TIP . J 4 HOH B 40 3042 71 HOH TIP . J 4 HOH B 41 3043 74 HOH TIP . J 4 HOH B 42 3044 75 HOH TIP . J 4 HOH B 43 3045 79 HOH TIP . J 4 HOH B 44 3046 80 HOH TIP . J 4 HOH B 45 3047 83 HOH TIP . J 4 HOH B 46 3048 84 HOH TIP . J 4 HOH B 47 3049 86 HOH TIP . # 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 CD1 YSA . . . H 3 20.752 166.44 213.871 1 40.72 ? CD1 YSA 3002 B 1 HETATM 2 C CE1 YSA . . . H 3 19.877 167.516 213.756 1 39.76 ? CE1 YSA 3002 B 1 HETATM 3 C CZ YSA . . . H 3 19.078 167.645 212.623 1 35.27 ? CZ YSA 3002 B 1 HETATM 4 O OH YSA . . . H 3 18.223 168.696 212.508 1 47.76 ? OH YSA 3002 B 1 HETATM 5 C CE2 YSA . . . H 3 19.151 166.696 211.607 1 36 ? CE2 YSA 3002 B 1 HETATM 6 C CD2 YSA . . . H 3 20.026 165.62 211.723 1 38.97 ? CD2 YSA 3002 B 1 HETATM 7 C CG YSA . . . H 3 20.829 165.494 212.853 1 40.14 ? CG YSA 3002 B 1 HETATM 8 C CB YSA . . . H 3 21.841 164.349 212.956 1 42.35 ? CB YSA 3002 B 1 HETATM 9 C CA YSA . . . H 3 21.176 162.971 212.962 1 47.69 ? CA YSA 3002 B 1 HETATM 10 N N YSA . . . H 3 20.327 162.828 214.155 1 48.2 ? N YSA 3002 B 1 HETATM 11 C C YSA . . . H 3 22.256 161.887 212.973 1 47.17 ? C YSA 3002 B 1 HETATM 12 O O YSA . . . H 3 22.327 161.074 213.892 1 55.63 ? O YSA 3002 B 1 HETATM 13 N NAT YSA . . . H 3 23.064 161.89 211.915 1 54.53 ? NAT YSA 3002 B 1 HETATM 14 S SBI YSA . . . H 3 24.272 160.803 211.789 1 36.66 ? SBI YSA 3002 B 1 HETATM 15 O OAD YSA . . . H 3 23.723 159.407 211.832 1 36.85 ? OAD YSA 3002 B 1 HETATM 16 O OAE YSA . . . H 3 25.226 160.996 212.931 1 44.46 ? OAE YSA 3002 B 1 HETATM 17 O O5' YSA . . . H 3 25.012 161.022 210.502 1 44.22 ? O5' YSA 3002 B 1 HETATM 18 C C5' YSA . . . H 3 24.924 160.091 209.418 1 44.9 ? C5' YSA 3002 B 1 HETATM 19 C C4' YSA . . . H 3 23.777 160.415 208.455 1 39.48 ? C4' YSA 3002 B 1 HETATM 20 O O4' YSA . . . H 3 23.864 159.569 207.294 1 49.5 ? O4' YSA 3002 B 1 HETATM 21 C C3' YSA . . . H 3 22.399 160.125 209.051 1 47.09 ? C3' YSA 3002 B 1 HETATM 22 O O3' YSA . . . H 3 21.38 160.777 208.287 1 34.88 ? O3' YSA 3002 B 1 HETATM 23 C C2' YSA . . . H 3 22.325 158.615 208.839 1 43.55 ? C2' YSA 3002 B 1 HETATM 24 O O2' YSA . . . H 3 20.951 158.218 208.84 1 35.77 ? O2' YSA 3002 B 1 HETATM 25 C C1' YSA . . . H 3 22.921 158.489 207.434 1 45.68 ? C1' YSA 3002 B 1 HETATM 26 N N9 YSA . . . H 3 23.59 157.176 207.26 1 41.37 ? N9 YSA 3002 B 1 HETATM 27 C C8 YSA . . . H 3 24.473 156.642 208.1 1 38.48 ? C8 YSA 3002 B 1 HETATM 28 N N7 YSA . . . H 3 24.894 155.466 207.638 1 41.19 ? N7 YSA 3002 B 1 HETATM 29 C C5 YSA . . . H 3 24.272 155.249 206.484 1 34.96 ? C5 YSA 3002 B 1 HETATM 30 C C4 YSA . . . H 3 23.441 156.333 206.241 1 34.95 ? C4 YSA 3002 B 1 HETATM 31 N N3 YSA . . . H 3 22.701 156.351 205.12 1 41.52 ? N3 YSA 3002 B 1 HETATM 32 C C2 YSA . . . H 3 22.757 155.358 204.251 1 46.29 ? C2 YSA 3002 B 1 HETATM 33 N N1 YSA . . . H 3 23.54 154.31 204.454 1 42.84 ? N1 YSA 3002 B 1 HETATM 34 C C6 YSA . . . H 3 24.307 154.221 205.55 1 32.63 ? C6 YSA 3002 B 1 HETATM 35 N N6 YSA . . . H 3 25.101 153.172 205.748 1 41.31 ? N6 YSA 3002 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 35 #