data_3KR1 # _model_server_result.job_id 6AzQNHrLHzUZ-1LpGws0lw _model_server_result.datetime_utc '2024-11-06 15:26:27' _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 3kr1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":3002}' # _entry.id 3KR1 # _exptl.entry_id 3KR1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _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 90 _cell.angle_gamma 90 _cell.entry_id 3KR1 _cell.length_a 94.054 _cell.length_b 94.054 _cell.length_c 189.44 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KR1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _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 ? 2 C N N ? 2 E 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 48 A CYS 48 1_555 B SG CYS 139 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 139 A CYS 139 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type non-polymer _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 277 n n N HN1 SAH sing 278 n n N HN2 SAH sing 279 n n CA CB SAH sing 280 n n CA C SAH sing 281 n n CA HA SAH sing 282 n n CB CG SAH sing 283 n n CB HB1 SAH sing 284 n n CB HB2 SAH sing 285 n n CG SD SAH sing 286 n n CG HG1 SAH sing 287 n n CG HG2 SAH sing 288 n n SD C5' SAH sing 289 n n C O SAH doub 290 n n C OXT SAH sing 291 n n OXT HXT SAH sing 292 n n C5' C4' SAH sing 293 n n C5' "H5'1" SAH sing 294 n n C5' "H5'2" SAH sing 295 n n C4' O4' SAH sing 296 n n C4' C3' SAH sing 297 n n C4' H4' SAH sing 298 n n O4' C1' SAH sing 299 n n C3' O3' SAH sing 300 n n C3' C2' SAH sing 301 n n C3' H3' SAH sing 302 n n O3' HO3' SAH sing 303 n n C2' O2' SAH sing 304 n n C2' C1' SAH sing 305 n n C2' H2' SAH sing 306 n n O2' HO2' SAH sing 307 n n C1' N9 SAH sing 308 n n C1' H1' SAH sing 309 n n N9 C8 SAH sing 310 n y N9 C4 SAH sing 311 n y C8 N7 SAH doub 312 n y C8 H8 SAH sing 313 n n N7 C5 SAH sing 314 n y C5 C6 SAH sing 315 n y C5 C4 SAH doub 316 n y C6 N6 SAH sing 317 n n C6 N1 SAH doub 318 n y N6 HN61 SAH sing 319 n n N6 HN62 SAH sing 320 n n N1 C2 SAH sing 321 n y C2 N3 SAH doub 322 n y C2 H2 SAH sing 323 n n N3 C4 SAH sing 324 n y # _atom_sites.entry_id 3KR1 _atom_sites.fract_transf_matrix[1][1] 0.010632 _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] 0.010632 _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] 0.005279 _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 SAH A 1 3001 3001 SAH SAH . D 3 VGD A 1 290 1 VGD VGD . E 2 SAH B 1 3002 3002 SAH SAH . F 3 VGD B 1 290 2 VGD VGD . G 4 HOH A 1 291 1 HOH HOH . G 4 HOH A 2 292 2 HOH HOH . G 4 HOH A 3 293 3 HOH HOH . G 4 HOH A 4 294 5 HOH HOH . G 4 HOH A 5 295 6 HOH HOH . G 4 HOH A 6 296 7 HOH HOH . G 4 HOH A 7 297 12 HOH HOH . G 4 HOH A 8 298 13 HOH HOH . G 4 HOH A 9 299 17 HOH HOH . G 4 HOH A 10 300 18 HOH HOH . G 4 HOH A 11 301 19 HOH HOH . G 4 HOH A 12 302 20 HOH HOH . G 4 HOH A 13 303 25 HOH HOH . G 4 HOH A 14 304 26 HOH HOH . G 4 HOH A 15 305 27 HOH HOH . G 4 HOH A 16 306 31 HOH HOH . G 4 HOH A 17 307 34 HOH HOH . G 4 HOH A 18 308 35 HOH HOH . G 4 HOH A 19 309 37 HOH HOH . G 4 HOH A 20 310 38 HOH HOH . G 4 HOH A 21 311 41 HOH HOH . G 4 HOH A 22 312 43 HOH HOH . G 4 HOH A 23 313 45 HOH HOH . G 4 HOH A 24 314 46 HOH HOH . G 4 HOH A 25 315 47 HOH HOH . G 4 HOH A 26 316 49 HOH HOH . G 4 HOH A 27 317 50 HOH HOH . G 4 HOH A 28 318 51 HOH HOH . G 4 HOH A 29 319 52 HOH HOH . G 4 HOH A 30 320 53 HOH HOH . G 4 HOH A 31 321 60 HOH HOH . G 4 HOH A 32 322 61 HOH HOH . G 4 HOH A 33 323 62 HOH HOH . G 4 HOH A 34 324 65 HOH HOH . G 4 HOH A 35 325 67 HOH HOH . G 4 HOH A 36 326 71 HOH HOH . G 4 HOH A 37 327 72 HOH HOH . G 4 HOH A 38 328 73 HOH HOH . G 4 HOH A 39 329 74 HOH HOH . G 4 HOH A 40 330 77 HOH HOH . G 4 HOH A 41 331 79 HOH HOH . G 4 HOH A 42 332 81 HOH HOH . G 4 HOH A 43 333 83 HOH HOH . G 4 HOH A 44 334 84 HOH HOH . G 4 HOH A 45 335 85 HOH HOH . G 4 HOH A 46 336 89 HOH HOH . G 4 HOH A 47 337 90 HOH HOH . G 4 HOH A 48 338 91 HOH HOH . G 4 HOH A 49 339 95 HOH HOH . G 4 HOH A 50 340 96 HOH HOH . G 4 HOH A 51 341 100 HOH HOH . G 4 HOH A 52 342 102 HOH HOH . G 4 HOH A 53 343 107 HOH HOH . G 4 HOH A 54 344 113 HOH HOH . G 4 HOH A 55 345 115 HOH HOH . G 4 HOH A 56 346 117 HOH HOH . G 4 HOH A 57 347 118 HOH HOH . G 4 HOH A 58 348 119 HOH HOH . G 4 HOH A 59 349 120 HOH HOH . G 4 HOH A 60 350 123 HOH HOH . G 4 HOH A 61 351 124 HOH HOH . G 4 HOH A 62 352 126 HOH HOH . G 4 HOH A 63 353 127 HOH HOH . G 4 HOH A 64 354 128 HOH HOH . G 4 HOH A 65 355 132 HOH HOH . G 4 HOH A 66 356 135 HOH HOH . G 4 HOH A 67 357 140 HOH HOH . G 4 HOH A 68 358 141 HOH HOH . G 4 HOH A 69 359 142 HOH HOH . G 4 HOH A 70 360 143 HOH HOH . G 4 HOH A 71 361 144 HOH HOH . G 4 HOH A 72 362 145 HOH HOH . G 4 HOH A 73 363 146 HOH HOH . H 4 HOH B 1 291 4 HOH HOH . H 4 HOH B 2 292 8 HOH HOH . H 4 HOH B 3 293 9 HOH HOH . H 4 HOH B 4 294 10 HOH HOH . H 4 HOH B 5 295 11 HOH HOH . H 4 HOH B 6 296 14 HOH HOH . H 4 HOH B 7 297 15 HOH HOH . H 4 HOH B 8 298 16 HOH HOH . H 4 HOH B 9 299 21 HOH HOH . H 4 HOH B 10 300 22 HOH HOH . H 4 HOH B 11 301 23 HOH HOH . H 4 HOH B 12 302 24 HOH HOH . H 4 HOH B 13 303 28 HOH HOH . H 4 HOH B 14 304 29 HOH HOH . H 4 HOH B 15 305 30 HOH HOH . H 4 HOH B 16 306 32 HOH HOH . H 4 HOH B 17 307 33 HOH HOH . H 4 HOH B 18 308 36 HOH HOH . H 4 HOH B 19 309 39 HOH HOH . H 4 HOH B 20 310 40 HOH HOH . H 4 HOH B 21 311 42 HOH HOH . H 4 HOH B 22 312 44 HOH HOH . H 4 HOH B 23 313 48 HOH HOH . H 4 HOH B 24 314 54 HOH HOH . H 4 HOH B 25 315 55 HOH HOH . H 4 HOH B 26 316 56 HOH HOH . H 4 HOH B 27 317 57 HOH HOH . H 4 HOH B 28 318 58 HOH HOH . H 4 HOH B 29 319 59 HOH HOH . H 4 HOH B 30 320 63 HOH HOH . H 4 HOH B 31 321 66 HOH HOH . H 4 HOH B 32 322 68 HOH HOH . H 4 HOH B 33 323 69 HOH HOH . H 4 HOH B 34 324 70 HOH HOH . H 4 HOH B 35 325 75 HOH HOH . H 4 HOH B 36 326 76 HOH HOH . H 4 HOH B 37 327 78 HOH HOH . H 4 HOH B 38 328 80 HOH HOH . H 4 HOH B 39 329 82 HOH HOH . H 4 HOH B 40 330 86 HOH HOH . H 4 HOH B 41 331 87 HOH HOH . H 4 HOH B 42 332 88 HOH HOH . H 4 HOH B 43 333 92 HOH HOH . H 4 HOH B 44 334 93 HOH HOH . H 4 HOH B 45 335 94 HOH HOH . H 4 HOH B 46 336 97 HOH HOH . H 4 HOH B 47 337 98 HOH HOH . H 4 HOH B 48 338 99 HOH HOH . H 4 HOH B 49 339 101 HOH HOH . H 4 HOH B 50 340 103 HOH HOH . H 4 HOH B 51 341 104 HOH HOH . H 4 HOH B 52 342 105 HOH HOH . H 4 HOH B 53 343 106 HOH HOH . H 4 HOH B 54 344 108 HOH HOH . H 4 HOH B 55 345 109 HOH HOH . H 4 HOH B 56 346 110 HOH HOH . H 4 HOH B 57 347 111 HOH HOH . H 4 HOH B 58 348 112 HOH HOH . H 4 HOH B 59 349 114 HOH HOH . H 4 HOH B 60 350 116 HOH HOH . H 4 HOH B 61 351 121 HOH HOH . H 4 HOH B 62 352 122 HOH HOH . H 4 HOH B 63 353 125 HOH HOH . H 4 HOH B 64 354 129 HOH HOH . H 4 HOH B 65 355 130 HOH HOH . H 4 HOH B 66 356 131 HOH HOH . H 4 HOH B 67 357 133 HOH HOH . H 4 HOH B 68 358 134 HOH HOH . H 4 HOH B 69 359 136 HOH HOH . H 4 HOH B 70 360 137 HOH HOH . H 4 HOH B 71 361 138 HOH HOH . H 4 HOH B 72 362 139 HOH HOH . H 4 HOH B 73 363 147 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 . . . E 2 28.131 50.654 -27.821 1 35.35 ? N SAH 3002 B 1 HETATM 2 C CA SAH . . . E 2 28.875 51.675 -27.105 1 39.18 ? CA SAH 3002 B 1 HETATM 3 C CB SAH . . . E 2 29.951 52.34 -27.967 1 39.6 ? CB SAH 3002 B 1 HETATM 4 C CG SAH . . . E 2 29.385 53.012 -29.22 1 41.03 ? CG SAH 3002 B 1 HETATM 5 S SD SAH . . . E 2 30.687 53.876 -30.169 1 45.43 ? SD SAH 3002 B 1 HETATM 6 C C SAH . . . E 2 27.944 52.691 -26.449 1 41.18 ? C SAH 3002 B 1 HETATM 7 O O SAH . . . E 2 26.854 52.311 -26.175 1 38.64 ? O SAH 3002 B 1 HETATM 8 O OXT SAH . . . E 2 28.572 53.813 -25.904 1 46.81 ? OXT SAH 3002 B 1 HETATM 9 C C5' SAH . . . E 2 30.435 53.164 -31.827 1 40.73 ? C5' SAH 3002 B 1 HETATM 10 C C4' SAH . . . E 2 31.328 51.971 -32.167 1 45.44 ? C4' SAH 3002 B 1 HETATM 11 O O4' SAH . . . E 2 31.266 51.665 -33.512 1 47.59 ? O4' SAH 3002 B 1 HETATM 12 C C3' SAH . . . E 2 32.817 52.142 -31.911 1 49.28 ? C3' SAH 3002 B 1 HETATM 13 O O3' SAH . . . E 2 33.179 51.316 -30.834 1 46.15 ? O3' SAH 3002 B 1 HETATM 14 C C2' SAH . . . E 2 33.386 51.694 -33.087 1 49.45 ? C2' SAH 3002 B 1 HETATM 15 O O2' SAH . . . E 2 34.592 51.004 -32.883 1 47.55 ? O2' SAH 3002 B 1 HETATM 16 C C1' SAH . . . E 2 32.381 50.877 -33.68 1 48.48 ? C1' SAH 3002 B 1 HETATM 17 N N9 SAH . . . E 2 32.527 50.65 -35.108 1 48.58 ? N9 SAH 3002 B 1 HETATM 18 C C8 SAH . . . E 2 33.218 51.396 -35.966 1 48.86 ? C8 SAH 3002 B 1 HETATM 19 N N7 SAH . . . E 2 33.053 50.867 -37.226 1 46.64 ? N7 SAH 3002 B 1 HETATM 20 C C5 SAH . . . E 2 32.236 49.78 -37.122 1 49.13 ? C5 SAH 3002 B 1 HETATM 21 C C6 SAH . . . E 2 31.759 48.905 -38.059 1 50.71 ? C6 SAH 3002 B 1 HETATM 22 N N6 SAH . . . E 2 32.113 49.071 -39.46 1 52.01 ? N6 SAH 3002 B 1 HETATM 23 N N1 SAH . . . E 2 30.959 47.905 -37.687 1 51.44 ? N1 SAH 3002 B 1 HETATM 24 C C2 SAH . . . E 2 30.619 47.755 -36.386 1 50.6 ? C2 SAH 3002 B 1 HETATM 25 N N3 SAH . . . E 2 31.096 48.625 -35.46 1 49.1 ? N3 SAH 3002 B 1 HETATM 26 C C4 SAH . . . E 2 31.899 49.631 -35.832 1 48.63 ? C4 SAH 3002 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #