data_3RJW # _model_server_result.job_id z6xBoUJM3j4Urxx1v_xdWQ _model_server_result.datetime_utc '2024-11-04 20:27:48' _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 3rjw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"CA","auth_seq_id":1198}' # _entry.id 3RJW # _exptl.entry_id 3RJW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 92.16 _cell.angle_gamma 90 _cell.entry_id 3RJW _cell.length_a 56.58 _cell.length_b 78.083 _cell.length_c 70.252 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RJW _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details 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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA _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 G N N ? 3 CA 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 B SG CYS 27 B CYS 937 1_555 B SG CYS 36 B CYS 946 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc1 A SG CYS 64 A CYS 974 1_555 C ZN ZN . A ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc2 A SG CYS 64 A CYS 974 1_555 E ZN ZN . A ZN 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc3 A SG CYS 66 A CYS 976 1_555 E ZN ZN . A ZN 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc4 A SG CYS 70 A CYS 980 1_555 D ZN ZN . A ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc5 A SG CYS 70 A CYS 980 1_555 E ZN ZN . A ZN 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc6 A SG CYS 75 A CYS 985 1_555 E ZN ZN . A ZN 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc7 A SG CYS 77 A CYS 987 1_555 C ZN ZN . A ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc8 A SG CYS 107 A CYS 1017 1_555 C ZN ZN . A ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc9 A SG CYS 107 A CYS 1017 1_555 D ZN ZN . A ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc10 A SG CYS 111 A CYS 1021 1_555 C ZN ZN . A ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc11 A SG CYS 113 A CYS 1023 1_555 D ZN ZN . A ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc12 A SG CYS 117 A CYS 1027 1_555 D ZN ZN . A ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc13 A SG CYS 205 A CYS 1115 1_555 F ZN ZN . A ZN 1397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc14 A SG CYS 258 A CYS 1168 1_555 F ZN ZN . A ZN 1397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc15 A SG CYS 260 A CYS 1170 1_555 F ZN ZN . A ZN 1397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc16 A SG CYS 265 A CYS 1175 1_555 F ZN ZN . A ZN 1397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc17 B SG CYS 64 B CYS 974 1_555 Y ZN ZN . B ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc18 B SG CYS 64 B CYS 974 1_555 AA ZN ZN . B ZN 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc19 B SG CYS 66 B CYS 976 1_555 AA ZN ZN . B ZN 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc20 B SG CYS 70 B CYS 980 1_555 Z ZN ZN . B ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc21 B SG CYS 70 B CYS 980 1_555 AA ZN ZN . B ZN 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc22 B SG CYS 75 B CYS 985 1_555 AA ZN ZN . B ZN 1396 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc23 B SG CYS 77 B CYS 987 1_555 Y ZN ZN . B ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc24 B SG CYS 107 B CYS 1017 1_555 Y ZN ZN . B ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc25 B SG CYS 107 B CYS 1017 1_555 Z ZN ZN . B ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc26 B SG CYS 111 B CYS 1021 1_555 Y ZN ZN . B ZN 1394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc27 B SG CYS 113 B CYS 1023 1_555 Z ZN ZN . B ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc28 B SG CYS 117 B CYS 1027 1_555 Z ZN ZN . B ZN 1395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc29 B SG CYS 205 B CYS 1115 1_555 BA ZN ZN . B ZN 1397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc30 B SG CYS 258 B CYS 1168 1_555 BA ZN ZN . B ZN 1397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc31 B SG CYS 260 B CYS 1170 1_555 BA ZN ZN . B ZN 1397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc32 B SG CYS 265 B CYS 1175 1_555 BA ZN ZN . B ZN 1397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms ? # 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 N CA SAH sing 365 n n N HN1 SAH sing 366 n n N HN2 SAH sing 367 n n CA CB SAH sing 368 n n CA C SAH sing 369 n n CA HA SAH sing 370 n n CB CG SAH sing 371 n n CB HB1 SAH sing 372 n n CB HB2 SAH sing 373 n n CG SD SAH sing 374 n n CG HG1 SAH sing 375 n n CG HG2 SAH sing 376 n n SD C5' SAH sing 377 n n C O SAH doub 378 n n C OXT SAH sing 379 n n OXT HXT SAH sing 380 n n C5' C4' SAH sing 381 n n C5' "H5'1" SAH sing 382 n n C5' "H5'2" SAH sing 383 n n C4' O4' SAH sing 384 n n C4' C3' SAH sing 385 n n C4' H4' SAH sing 386 n n O4' C1' SAH sing 387 n n C3' O3' SAH sing 388 n n C3' C2' SAH sing 389 n n C3' H3' SAH sing 390 n n O3' HO3' SAH sing 391 n n C2' O2' SAH sing 392 n n C2' C1' SAH sing 393 n n C2' H2' SAH sing 394 n n O2' HO2' SAH sing 395 n n C1' N9 SAH sing 396 n n C1' H1' SAH sing 397 n n N9 C8 SAH sing 398 n y N9 C4 SAH sing 399 n y C8 N7 SAH doub 400 n y C8 H8 SAH sing 401 n n N7 C5 SAH sing 402 n y C5 C6 SAH sing 403 n y C5 C4 SAH doub 404 n y C6 N6 SAH sing 405 n n C6 N1 SAH doub 406 n y N6 HN61 SAH sing 407 n n N6 HN62 SAH sing 408 n n N1 C2 SAH sing 409 n y C2 N3 SAH doub 410 n y C2 H2 SAH sing 411 n n N3 C4 SAH sing 412 n y # _atom_sites.entry_id 3RJW _atom_sites.fract_transf_matrix[1][1] 0.017674 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000667 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012807 _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] 0.014245 _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 ZN A 1 1394 1394 ZN ZN . D 2 ZN A 1 1395 1395 ZN ZN . E 2 ZN A 1 1396 1396 ZN ZN . F 2 ZN A 1 1397 1397 ZN ZN . G 3 SAH A 1 1198 1198 SAH SAH . H 4 CIQ A 1 2000 2000 CIQ CIQ . I 5 UNX A 1 4 4 UNX UNX . J 5 UNX A 1 5 5 UNX UNX . K 5 UNX A 1 7 7 UNX UNX . L 5 UNX A 1 8 8 UNX UNX . M 5 UNX A 1 9 9 UNX UNX . N 5 UNX A 1 10 10 UNX UNX . O 5 UNX A 1 4247 4247 UNX UNX . P 5 UNX A 1 4248 4248 UNX UNX . Q 5 UNX A 1 4255 4255 UNX UNX . R 5 UNX A 1 4256 4256 UNX UNX . S 5 UNX A 1 4257 4257 UNX UNX . T 5 UNX A 1 4258 4258 UNX UNX . U 5 UNX A 1 4259 4259 UNX UNX . V 5 UNX A 1 4260 4260 UNX UNX . W 5 UNX A 1 4263 4263 UNX UNX . X 5 UNX A 1 4302 4302 UNX UNX . Y 2 ZN B 1 1394 1394 ZN ZN . Z 2 ZN B 1 1395 1395 ZN ZN . AA 2 ZN B 1 1396 1396 ZN ZN . BA 2 ZN B 1 1397 1397 ZN ZN . CA 3 SAH B 1 1198 1198 SAH SAH . DA 4 CIQ B 1 2000 2000 CIQ CIQ . EA 5 UNX B 1 1 1 UNX UNX . FA 5 UNX B 1 2 2 UNX UNX . GA 5 UNX B 1 3 3 UNX UNX . HA 5 UNX B 1 6 6 UNX UNX . IA 5 UNX B 1 4261 4261 UNX UNX . JA 5 UNX B 1 4262 4262 UNX UNX . KA 5 UNX B 1 4264 4264 UNX UNX . LA 5 UNX B 1 4265 4265 UNX UNX . MA 5 UNX B 1 4266 4266 UNX UNX . NA 5 UNX B 1 4303 4303 UNX UNX . OA 5 UNX B 1 4304 4304 UNX UNX . PA 5 UNX B 1 4305 4305 UNX UNX . QA 5 UNX B 1 4306 4306 UNX UNX . RA 6 HOH A 1 1 1 HOH HOH . RA 6 HOH A 2 2 2 HOH HOH . RA 6 HOH A 3 3 3 HOH HOH . RA 6 HOH A 4 6 6 HOH HOH . RA 6 HOH A 5 11 11 HOH HOH . RA 6 HOH A 6 13 13 HOH HOH . RA 6 HOH A 7 14 14 HOH HOH . RA 6 HOH A 8 15 15 HOH HOH . RA 6 HOH A 9 19 19 HOH HOH . RA 6 HOH A 10 25 25 HOH HOH . RA 6 HOH A 11 26 26 HOH HOH . RA 6 HOH A 12 28 28 HOH HOH . RA 6 HOH A 13 29 29 HOH HOH . RA 6 HOH A 14 33 33 HOH HOH . RA 6 HOH A 15 35 35 HOH HOH . RA 6 HOH A 16 38 38 HOH HOH . RA 6 HOH A 17 39 39 HOH HOH . RA 6 HOH A 18 1194 2 HOH HOH . RA 6 HOH A 19 1195 7 HOH HOH . RA 6 HOH A 20 1196 8 HOH HOH . RA 6 HOH A 21 1197 9 HOH HOH . RA 6 HOH A 22 1199 1199 HOH HOH . RA 6 HOH A 23 1200 1200 HOH HOH . RA 6 HOH A 24 1201 10 HOH HOH . SA 6 HOH B 1 4 4 HOH HOH . SA 6 HOH B 2 5 5 HOH HOH . SA 6 HOH B 3 8 8 HOH HOH . SA 6 HOH B 4 10 10 HOH HOH . SA 6 HOH B 5 12 12 HOH HOH . SA 6 HOH B 6 13 13 HOH HOH . SA 6 HOH B 7 16 16 HOH HOH . SA 6 HOH B 8 17 17 HOH HOH . SA 6 HOH B 9 18 18 HOH HOH . SA 6 HOH B 10 20 20 HOH HOH . SA 6 HOH B 11 23 23 HOH HOH . SA 6 HOH B 12 24 24 HOH HOH . SA 6 HOH B 13 27 27 HOH HOH . SA 6 HOH B 14 31 31 HOH HOH . SA 6 HOH B 15 32 32 HOH HOH . SA 6 HOH B 16 34 34 HOH HOH . SA 6 HOH B 17 36 36 HOH HOH . SA 6 HOH B 18 1194 4 HOH HOH . SA 6 HOH B 19 1195 5 HOH HOH . SA 6 HOH B 20 1196 6 HOH HOH . SA 6 HOH B 21 1197 12 HOH HOH . SA 6 HOH B 22 1199 1199 HOH HOH . SA 6 HOH B 23 1201 1201 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 N N SAH . . . CA 3 27.772 -0.895 9.363 1 51.81 ? N SAH 1198 B 1 HETATM 2 C CA SAH . . . CA 3 27.421 -0.002 10.451 1 51.92 ? CA SAH 1198 B 1 HETATM 3 C CB SAH . . . CA 3 25.917 -0.042 10.722 1 50.66 ? CB SAH 1198 B 1 HETATM 4 C CG SAH . . . CA 3 25.13 0.639 9.623 1 51.55 ? CG SAH 1198 B 1 HETATM 5 S SD SAH . . . CA 3 24.884 2.416 9.996 1 52.16 ? SD SAH 1198 B 1 HETATM 6 C C SAH . . . CA 3 28.307 -0.172 11.695 1 53.02 ? C SAH 1198 B 1 HETATM 7 O O SAH . . . CA 3 28.086 0.427 12.736 1 52.28 ? O SAH 1198 B 1 HETATM 8 O OXT SAH . . . CA 3 29.373 -0.982 11.622 1 54.25 ? OXT SAH 1198 B 1 HETATM 9 C C5' SAH . . . CA 3 25.348 3.176 8.409 1 53.48 ? C5' SAH 1198 B 1 HETATM 10 C C4' SAH . . . CA 3 26.85 3 8.052 1 54.17 ? C4' SAH 1198 B 1 HETATM 11 O O4' SAH . . . CA 3 27.223 1.614 7.769 1 53.08 ? O4' SAH 1198 B 1 HETATM 12 C C3' SAH . . . CA 3 27.187 3.692 6.749 1 55.73 ? C3' SAH 1198 B 1 HETATM 13 O O3' SAH . . . CA 3 27.332 5.061 6.958 1 56.62 ? O3' SAH 1198 B 1 HETATM 14 C C2' SAH . . . CA 3 28.529 3.01 6.414 1 55.54 ? C2' SAH 1198 B 1 HETATM 15 O O2' SAH . . . CA 3 29.535 3.331 7.372 1 56.34 ? O2' SAH 1198 B 1 HETATM 16 C C1' SAH . . . CA 3 28.121 1.534 6.633 1 54.8 ? C1' SAH 1198 B 1 HETATM 17 N N9 SAH . . . CA 3 27.431 0.94 5.493 1 55.37 ? N9 SAH 1198 B 1 HETATM 18 C C8 SAH . . . CA 3 26.138 0.531 5.464 1 54.67 ? C8 SAH 1198 B 1 HETATM 19 N N7 SAH . . . CA 3 25.847 0.026 4.307 1 56.45 ? N7 SAH 1198 B 1 HETATM 20 C C5 SAH . . . CA 3 26.91 0.077 3.504 1 57.05 ? C5 SAH 1198 B 1 HETATM 21 C C6 SAH . . . CA 3 27.155 -0.282 2.16 1 58.9 ? C6 SAH 1198 B 1 HETATM 22 N N6 SAH . . . CA 3 26.195 -0.858 1.403 1 59.72 ? N6 SAH 1198 B 1 HETATM 23 N N1 SAH . . . CA 3 28.397 -0.064 1.658 1 59.79 ? N1 SAH 1198 B 1 HETATM 24 C C2 SAH . . . CA 3 29.389 0.498 2.408 1 59.89 ? C2 SAH 1198 B 1 HETATM 25 N N3 SAH . . . CA 3 29.168 0.857 3.685 1 57.78 ? N3 SAH 1198 B 1 HETATM 26 C C4 SAH . . . CA 3 27.964 0.669 4.264 1 56.88 ? C4 SAH 1198 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #