data_4XVY
#
_model_server_result.job_id            PKYvV3w4cP0QzxrPmPrFYA 
_model_server_result.datetime_utc      '2024-10-16 21:36:21' 
_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          4xvy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":302}' 
#
_entry.id    4XVY 
#
_exptl.entry_id    4XVY 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            4XVY 
_cell.length_a            50.057 
_cell.length_b            89.892 
_cell.length_c            127.655 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XVY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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
? 3 D N N 
? 3 F 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
metalc ? metalc1 A OD1 ASP 209 A ASP 189 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? 
metalc ? metalc2 A OD1 ASP 211 A ASP 191 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? 
metalc ? metalc3 A OD2 ASP 236 A ASP 216 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc4 A OD2 ASP 237 A ASP 217 1_555 C MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc5 C MG MG . A MG 301 1_555 G O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc6 C MG MG . A MG 301 1_555 G O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? 
metalc ? metalc7 C MG MG . A MG 301 1_555 G O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc8 B OD1 ASP 209 B ASP 189 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? 
metalc ? metalc9 B OD1 ASP 211 B ASP 191 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc10 B OD2 ASP 236 B ASP 216 1_555 E MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc11 E MG MG . B MG 301 1_555 H O HOH . B HOH 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? 
metalc ? metalc12 E MG MG . B MG 301 1_555 H O HOH . B HOH 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? 
metalc ? metalc13 E MG MG . B MG 301 1_555 H O HOH . B HOH 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
#
_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 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                     4XVY 
_atom_sites.fract_transf_matrix[1][1]    0.019977 
_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]    0.011124 
_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]    0.007834 
_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 MG A 1 301 2 MG MG . 
D 3 SAH A 1 302 2 SAH SAH . 
E 2 MG B 1 301 1 MG MG . 
F 3 SAH B 1 302 1 SAH SAH . 
G 4 HOH A 1 401 60 HOH HOH . 
G 4 HOH A 2 402 38 HOH HOH . 
G 4 HOH A 3 403 9 HOH HOH . 
G 4 HOH A 4 404 55 HOH HOH . 
G 4 HOH A 5 405 56 HOH HOH . 
G 4 HOH A 6 406 57 HOH HOH . 
G 4 HOH A 7 407 58 HOH HOH . 
G 4 HOH A 8 408 59 HOH HOH . 
G 4 HOH A 9 409 61 HOH HOH . 
G 4 HOH A 10 410 62 HOH HOH . 
G 4 HOH A 11 411 63 HOH HOH . 
G 4 HOH A 12 412 64 HOH HOH . 
H 4 HOH B 1 401 46 HOH HOH . 
H 4 HOH B 2 402 47 HOH HOH . 
H 4 HOH B 3 403 34 HOH HOH . 
H 4 HOH B 4 404 2 HOH HOH . 
H 4 HOH B 5 405 3 HOH HOH . 
H 4 HOH B 6 406 4 HOH HOH . 
H 4 HOH B 7 407 6 HOH HOH . 
H 4 HOH B 8 408 11 HOH HOH . 
H 4 HOH B 9 409 12 HOH HOH . 
H 4 HOH B 10 410 18 HOH HOH . 
H 4 HOH B 11 411 20 HOH HOH . 
H 4 HOH B 12 412 23 HOH HOH . 
H 4 HOH B 13 413 24 HOH HOH . 
H 4 HOH B 14 414 26 HOH HOH . 
H 4 HOH B 15 415 27 HOH HOH . 
H 4 HOH B 16 416 29 HOH HOH . 
H 4 HOH B 17 417 37 HOH HOH . 
H 4 HOH B 18 418 39 HOH HOH . 
H 4 HOH B 19 419 40 HOH HOH . 
H 4 HOH B 20 420 44 HOH HOH . 
H 4 HOH B 21 421 52 HOH HOH . 
H 4 HOH B 22 422 53 HOH HOH . 
H 4 HOH B 23 423 54 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 . . . D 3 -16.974 -5.967 -29.106 1 31.54 ? N SAH 302 A 1 
HETATM 2 C CA SAH . . . D 3 -17.134 -7.155 -30.026 1 33.66 ? CA SAH 302 A 1 
HETATM 3 C CB SAH . . . D 3 -17.233 -8.478 -29.207 1 35.39 ? CB SAH 302 A 1 
HETATM 4 C CG SAH . . . D 3 -16.055 -8.774 -28.242 1 36.29 ? CG SAH 302 A 1 
HETATM 5 S SD SAH . . . D 3 -15.887 -10.534 -27.923 1 45.57 ? SD SAH 302 A 1 
HETATM 6 C C SAH . . . D 3 -18.302 -6.87 -30.976 1 33.4 ? C SAH 302 A 1 
HETATM 7 O O SAH . . . D 3 -18.958 -7.799 -31.509 1 30.45 ? O SAH 302 A 1 
HETATM 8 O OXT SAH . . . D 3 -18.613 -5.67 -31.232 1 31.56 ? OXT SAH 302 A 1 
HETATM 9 C C5' SAH . . . D 3 -14.487 -10.591 -26.817 1 51.64 ? C5' SAH 302 A 1 
HETATM 10 C C4' SAH . . . D 3 -13.163 -10.356 -27.581 1 52.26 ? C4' SAH 302 A 1 
HETATM 11 O O4' SAH . . . D 3 -12.055 -10.017 -26.761 1 54.5 ? O4' SAH 302 A 1 
HETATM 12 C C3' SAH . . . D 3 -12.715 -11.58 -28.333 1 48.35 ? C3' SAH 302 A 1 
HETATM 13 O O3' SAH . . . D 3 -12.549 -11.072 -29.637 1 49.27 ? O3' SAH 302 A 1 
HETATM 14 C C2' SAH . . . D 3 -11.384 -12.055 -27.776 1 50.67 ? C2' SAH 302 A 1 
HETATM 15 O O2' SAH . . . D 3 -10.462 -12.384 -28.833 1 50.17 ? O2' SAH 302 A 1 
HETATM 16 C C1' SAH . . . D 3 -10.892 -10.846 -27.008 1 53.85 ? C1' SAH 302 A 1 
HETATM 17 N N9 SAH . . . D 3 -10.23 -11.044 -25.681 1 57.64 ? N9 SAH 302 A 1 
HETATM 18 C C8 SAH . . . D 3 -10.749 -11.69 -24.634 1 54.6 ? C8 SAH 302 A 1 
HETATM 19 N N7 SAH . . . D 3 -9.907 -11.615 -23.576 1 58.48 ? N7 SAH 302 A 1 
HETATM 20 C C5 SAH . . . D 3 -8.836 -10.883 -23.927 1 55.01 ? C5 SAH 302 A 1 
HETATM 21 C C6 SAH . . . D 3 -7.579 -10.414 -23.291 1 55.77 ? C6 SAH 302 A 1 
HETATM 22 N N6 SAH . . . D 3 -7.276 -10.718 -22.011 1 53.89 ? N6 SAH 302 A 1 
HETATM 23 N N1 SAH . . . D 3 -6.725 -9.659 -24.026 1 58.44 ? N1 SAH 302 A 1 
HETATM 24 C C2 SAH . . . D 3 -6.991 -9.35 -25.302 1 56.66 ? C2 SAH 302 A 1 
HETATM 25 N N3 SAH . . . D 3 -8.111 -9.75 -25.93 1 57.95 ? N3 SAH 302 A 1 
HETATM 26 C C4 SAH . . . D 3 -9.057 -10.497 -25.315 1 56.41 ? C4 SAH 302 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           251 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           26 
#