data_3KQY
#
_model_server_result.job_id            E2zkBJrWmYTaRsktmzFoZw 
_model_server_result.datetime_utc      '2024-11-04 23:08:01' 
_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          3kqy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":3002}' 
#
_entry.id    3KQY 
#
_exptl.entry_id    3KQY 
_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            3KQY 
_cell.length_a            94.525 
_cell.length_b            94.525 
_cell.length_c            188.27 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KQY 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf2 A SG CYS 139 A CYS 139 1_555 B SG CYS 48 B CYS 48 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
#
_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 296 n n 
N HN1 SAH sing 297 n n 
N HN2 SAH sing 298 n n 
CA CB SAH sing 299 n n 
CA C SAH sing 300 n n 
CA HA SAH sing 301 n n 
CB CG SAH sing 302 n n 
CB HB1 SAH sing 303 n n 
CB HB2 SAH sing 304 n n 
CG SD SAH sing 305 n n 
CG HG1 SAH sing 306 n n 
CG HG2 SAH sing 307 n n 
SD C5' SAH sing 308 n n 
C O SAH doub 309 n n 
C OXT SAH sing 310 n n 
OXT HXT SAH sing 311 n n 
C5' C4' SAH sing 312 n n 
C5' "H5'1" SAH sing 313 n n 
C5' "H5'2" SAH sing 314 n n 
C4' O4' SAH sing 315 n n 
C4' C3' SAH sing 316 n n 
C4' H4' SAH sing 317 n n 
O4' C1' SAH sing 318 n n 
C3' O3' SAH sing 319 n n 
C3' C2' SAH sing 320 n n 
C3' H3' SAH sing 321 n n 
O3' HO3' SAH sing 322 n n 
C2' O2' SAH sing 323 n n 
C2' C1' SAH sing 324 n n 
C2' H2' SAH sing 325 n n 
O2' HO2' SAH sing 326 n n 
C1' N9 SAH sing 327 n n 
C1' H1' SAH sing 328 n n 
N9 C8 SAH sing 329 n y 
N9 C4 SAH sing 330 n y 
C8 N7 SAH doub 331 n y 
C8 H8 SAH sing 332 n n 
N7 C5 SAH sing 333 n y 
C5 C6 SAH sing 334 n y 
C5 C4 SAH doub 335 n y 
C6 N6 SAH sing 336 n n 
C6 N1 SAH doub 337 n y 
N6 HN61 SAH sing 338 n n 
N6 HN62 SAH sing 339 n n 
N1 C2 SAH sing 340 n y 
C2 N3 SAH doub 341 n y 
C2 H2 SAH sing 342 n n 
N3 C4 SAH sing 343 n y 
#
_atom_sites.entry_id                     3KQY 
_atom_sites.fract_transf_matrix[1][1]    0.010579 
_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]    0.010579 
_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]    0.005312 
_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 ES0 A 1 290 1 ES0 ES0 . 
E 2 SAH B 1 3002 3002 SAH SAH . 
F 3 ES0 B 1 290 2 ES0 ES0 . 
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 4 HOH HOH . 
G 4 HOH A 5 295 5 HOH HOH . 
G 4 HOH A 6 296 12 HOH HOH . 
G 4 HOH A 7 297 14 HOH HOH . 
G 4 HOH A 8 298 19 HOH HOH . 
G 4 HOH A 9 299 21 HOH HOH . 
G 4 HOH A 10 300 25 HOH HOH . 
G 4 HOH A 11 301 28 HOH HOH . 
G 4 HOH A 12 302 31 HOH HOH . 
G 4 HOH A 13 303 33 HOH HOH . 
G 4 HOH A 14 304 34 HOH HOH . 
G 4 HOH A 15 305 36 HOH HOH . 
G 4 HOH A 16 306 37 HOH HOH . 
G 4 HOH A 17 307 39 HOH HOH . 
G 4 HOH A 18 308 40 HOH HOH . 
G 4 HOH A 19 309 43 HOH HOH . 
G 4 HOH A 20 310 45 HOH HOH . 
G 4 HOH A 21 311 48 HOH HOH . 
G 4 HOH A 22 312 50 HOH HOH . 
G 4 HOH A 23 313 52 HOH HOH . 
G 4 HOH A 24 314 53 HOH HOH . 
G 4 HOH A 25 315 59 HOH HOH . 
G 4 HOH A 26 316 64 HOH HOH . 
G 4 HOH A 27 317 66 HOH HOH . 
G 4 HOH A 28 318 71 HOH HOH . 
G 4 HOH A 29 319 72 HOH HOH . 
G 4 HOH A 30 320 76 HOH HOH . 
G 4 HOH A 31 321 81 HOH HOH . 
G 4 HOH A 32 322 86 HOH HOH . 
G 4 HOH A 33 323 89 HOH HOH . 
G 4 HOH A 34 324 90 HOH HOH . 
G 4 HOH A 35 325 92 HOH HOH . 
G 4 HOH A 36 326 94 HOH HOH . 
G 4 HOH A 37 327 97 HOH HOH . 
G 4 HOH A 38 328 99 HOH HOH . 
G 4 HOH A 39 329 100 HOH HOH . 
G 4 HOH A 40 330 105 HOH HOH . 
G 4 HOH A 41 331 107 HOH HOH . 
G 4 HOH A 42 332 108 HOH HOH . 
G 4 HOH A 43 333 109 HOH HOH . 
G 4 HOH A 44 334 110 HOH HOH . 
G 4 HOH A 45 335 111 HOH HOH . 
G 4 HOH A 46 336 115 HOH HOH . 
G 4 HOH A 47 337 117 HOH HOH . 
G 4 HOH A 48 338 120 HOH HOH . 
G 4 HOH A 49 339 127 HOH HOH . 
G 4 HOH A 50 340 129 HOH HOH . 
G 4 HOH A 51 341 130 HOH HOH . 
G 4 HOH A 52 342 132 HOH HOH . 
G 4 HOH A 53 343 133 HOH HOH . 
G 4 HOH A 54 344 143 HOH HOH . 
G 4 HOH A 55 345 148 HOH HOH . 
G 4 HOH A 56 346 149 HOH HOH . 
G 4 HOH A 57 347 150 HOH HOH . 
G 4 HOH A 58 348 151 HOH HOH . 
G 4 HOH A 59 349 152 HOH HOH . 
G 4 HOH A 60 350 157 HOH HOH . 
G 4 HOH A 61 351 166 HOH HOH . 
G 4 HOH A 62 352 167 HOH HOH . 
G 4 HOH A 63 353 172 HOH HOH . 
G 4 HOH A 64 354 173 HOH HOH . 
G 4 HOH A 65 355 175 HOH HOH . 
G 4 HOH A 66 356 178 HOH HOH . 
G 4 HOH A 67 357 181 HOH HOH . 
G 4 HOH A 68 358 187 HOH HOH . 
G 4 HOH A 69 359 188 HOH HOH . 
G 4 HOH A 70 360 190 HOH HOH . 
G 4 HOH A 71 361 197 HOH HOH . 
G 4 HOH A 72 362 198 HOH HOH . 
G 4 HOH A 73 363 199 HOH HOH . 
H 4 HOH B 1 291 6 HOH HOH . 
H 4 HOH B 2 292 7 HOH HOH . 
H 4 HOH B 3 293 8 HOH HOH . 
H 4 HOH B 4 294 9 HOH HOH . 
H 4 HOH B 5 295 10 HOH HOH . 
H 4 HOH B 6 296 11 HOH HOH . 
H 4 HOH B 7 297 13 HOH HOH . 
H 4 HOH B 8 298 15 HOH HOH . 
H 4 HOH B 9 299 18 HOH HOH . 
H 4 HOH B 10 300 20 HOH HOH . 
H 4 HOH B 11 301 22 HOH HOH . 
H 4 HOH B 12 302 23 HOH HOH . 
H 4 HOH B 13 303 24 HOH HOH . 
H 4 HOH B 14 304 26 HOH HOH . 
H 4 HOH B 15 305 27 HOH HOH . 
H 4 HOH B 16 306 29 HOH HOH . 
H 4 HOH B 17 307 30 HOH HOH . 
H 4 HOH B 18 308 32 HOH HOH . 
H 4 HOH B 19 309 35 HOH HOH . 
H 4 HOH B 20 310 41 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 49 HOH HOH . 
H 4 HOH B 24 314 51 HOH HOH . 
H 4 HOH B 25 315 54 HOH HOH . 
H 4 HOH B 26 316 55 HOH HOH . 
H 4 HOH B 27 317 56 HOH HOH . 
H 4 HOH B 28 318 57 HOH HOH . 
H 4 HOH B 29 319 58 HOH HOH . 
H 4 HOH B 30 320 60 HOH HOH . 
H 4 HOH B 31 321 61 HOH HOH . 
H 4 HOH B 32 322 63 HOH HOH . 
H 4 HOH B 33 323 65 HOH HOH . 
H 4 HOH B 34 324 67 HOH HOH . 
H 4 HOH B 35 325 68 HOH HOH . 
H 4 HOH B 36 326 69 HOH HOH . 
H 4 HOH B 37 327 70 HOH HOH . 
H 4 HOH B 38 328 73 HOH HOH . 
H 4 HOH B 39 329 74 HOH HOH . 
H 4 HOH B 40 330 78 HOH HOH . 
H 4 HOH B 41 331 80 HOH HOH . 
H 4 HOH B 42 332 82 HOH HOH . 
H 4 HOH B 43 333 83 HOH HOH . 
H 4 HOH B 44 334 84 HOH HOH . 
H 4 HOH B 45 335 85 HOH HOH . 
H 4 HOH B 46 336 87 HOH HOH . 
H 4 HOH B 47 337 88 HOH HOH . 
H 4 HOH B 48 338 91 HOH HOH . 
H 4 HOH B 49 339 93 HOH HOH . 
H 4 HOH B 50 340 95 HOH HOH . 
H 4 HOH B 51 341 96 HOH HOH . 
H 4 HOH B 52 342 98 HOH HOH . 
H 4 HOH B 53 343 103 HOH HOH . 
H 4 HOH B 54 344 104 HOH HOH . 
H 4 HOH B 55 345 113 HOH HOH . 
H 4 HOH B 56 346 114 HOH HOH . 
H 4 HOH B 57 347 116 HOH HOH . 
H 4 HOH B 58 348 118 HOH HOH . 
H 4 HOH B 59 349 121 HOH HOH . 
H 4 HOH B 60 350 124 HOH HOH . 
H 4 HOH B 61 351 126 HOH HOH . 
H 4 HOH B 62 352 128 HOH HOH . 
H 4 HOH B 63 353 135 HOH HOH . 
H 4 HOH B 64 354 136 HOH HOH . 
H 4 HOH B 65 355 137 HOH HOH . 
H 4 HOH B 66 356 138 HOH HOH . 
H 4 HOH B 67 357 140 HOH HOH . 
H 4 HOH B 68 358 142 HOH HOH . 
H 4 HOH B 69 359 147 HOH HOH . 
H 4 HOH B 70 360 153 HOH HOH . 
H 4 HOH B 71 361 154 HOH HOH . 
H 4 HOH B 72 362 155 HOH HOH . 
H 4 HOH B 73 363 156 HOH HOH . 
H 4 HOH B 74 364 159 HOH HOH . 
H 4 HOH B 75 365 163 HOH HOH . 
H 4 HOH B 76 366 165 HOH HOH . 
H 4 HOH B 77 367 168 HOH HOH . 
H 4 HOH B 78 368 169 HOH HOH . 
H 4 HOH B 79 369 170 HOH HOH . 
H 4 HOH B 80 370 174 HOH HOH . 
H 4 HOH B 81 371 179 HOH HOH . 
H 4 HOH B 82 372 184 HOH HOH . 
H 4 HOH B 83 373 186 HOH HOH . 
H 4 HOH B 84 374 191 HOH HOH . 
H 4 HOH B 85 375 192 HOH HOH . 
H 4 HOH B 86 376 193 HOH HOH . 
H 4 HOH B 87 377 194 HOH HOH . 
H 4 HOH B 88 378 195 HOH HOH . 
H 4 HOH B 89 379 196 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 28.158 51.15 -27.613 1 34.7 ? N SAH 3002 B 1 
HETATM 2 C CA SAH . . . E 2 28.992 52.099 -26.888 1 36.93 ? CA SAH 3002 B 1 
HETATM 3 C CB SAH . . . E 2 29.972 52.868 -27.792 1 37.52 ? CB SAH 3002 B 1 
HETATM 4 C CG SAH . . . E 2 29.304 53.6 -28.967 1 38.24 ? CG SAH 3002 B 1 
HETATM 5 S SD SAH . . . E 2 30.48 54.616 -29.929 1 46.87 ? SD SAH 3002 B 1 
HETATM 6 C C SAH . . . E 2 28.129 53.02 -26.044 1 36.07 ? C SAH 3002 B 1 
HETATM 7 O O SAH . . . E 2 26.985 52.717 -25.974 1 33.88 ? O SAH 3002 B 1 
HETATM 8 O OXT SAH . . . E 2 28.685 54.254 -25.685 1 37 ? OXT SAH 3002 B 1 
HETATM 9 C C5' SAH . . . E 2 30.364 53.825 -31.562 1 45.21 ? C5' SAH 3002 B 1 
HETATM 10 C C4' SAH . . . E 2 31.284 52.633 -31.815 1 45.42 ? C4' SAH 3002 B 1 
HETATM 11 O O4' SAH . . . E 2 31.166 52.253 -33.138 1 44.87 ? O4' SAH 3002 B 1 
HETATM 12 C C3' SAH . . . E 2 32.783 52.747 -31.586 1 45.45 ? C3' SAH 3002 B 1 
HETATM 13 O O3' SAH . . . E 2 33.118 51.808 -30.591 1 36.4 ? O3' SAH 3002 B 1 
HETATM 14 C C2' SAH . . . E 2 33.309 52.368 -32.814 1 44.38 ? C2' SAH 3002 B 1 
HETATM 15 O O2' SAH . . . E 2 34.549 51.706 -32.737 1 43.46 ? O2' SAH 3002 B 1 
HETATM 16 C C1' SAH . . . E 2 32.309 51.521 -33.374 1 44.02 ? C1' SAH 3002 B 1 
HETATM 17 N N9 SAH . . . E 2 32.448 51.273 -34.8 1 49.22 ? N9 SAH 3002 B 1 
HETATM 18 C C8 SAH . . . E 2 33.133 52.028 -35.656 1 50.14 ? C8 SAH 3002 B 1 
HETATM 19 N N7 SAH . . . E 2 32.982 51.479 -36.912 1 49.68 ? N7 SAH 3002 B 1 
HETATM 20 C C5 SAH . . . E 2 32.188 50.374 -36.81 1 52.7 ? C5 SAH 3002 B 1 
HETATM 21 C C6 SAH . . . E 2 31.736 49.481 -37.746 1 54.79 ? C6 SAH 3002 B 1 
HETATM 22 N N6 SAH . . . E 2 32.096 49.64 -39.146 1 56.56 ? N6 SAH 3002 B 1 
HETATM 23 N N1 SAH . . . E 2 30.956 48.466 -37.377 1 56.62 ? N1 SAH 3002 B 1 
HETATM 24 C C2 SAH . . . E 2 30.615 48.325 -36.073 1 52.07 ? C2 SAH 3002 B 1 
HETATM 25 N N3 SAH . . . E 2 31.066 49.215 -35.15 1 48.15 ? N3 SAH 3002 B 1 
HETATM 26 C C4 SAH . . . E 2 31.848 50.233 -35.521 1 50.44 ? C4 SAH 3002 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#