data_7U5V
#
_model_server_result.job_id            7ID-47OOhRhWpRwzT9mSWQ 
_model_server_result.datetime_utc      '2025-04-01 18:47:13' 
_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          7u5v 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":4002}' 
#
_entry.id    7U5V 
#
_exptl.entry_id    7U5V 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              384.411 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-ADENOSYL-L-HOMOCYSTEINE 
_entity.pdbx_number_of_molecules    1 
_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            7U5V 
_cell.length_a            54.48 
_cell.length_b            54.48 
_cell.length_c            105.63 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7U5V 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    'P 32 2"' 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
covale ? covale1 B C VAL 6 C VAL 3956 1_555 B N MLZ 7 C MLZ 3957 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale2 B C MLZ 7 C MLZ 3957 1_555 B N ARG 8 C ARG 3958 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? 
metalc ? metalc1 A SG CYS 99 A CYS 3909 1_555 C ZN ZN . A ZN 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 
#
_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 301 n n 
N HN1 SAH sing 302 n n 
N HN2 SAH sing 303 n n 
CA CB SAH sing 304 n n 
CA C SAH sing 305 n n 
CA HA SAH sing 306 n n 
CB CG SAH sing 307 n n 
CB HB1 SAH sing 308 n n 
CB HB2 SAH sing 309 n n 
CG SD SAH sing 310 n n 
CG HG1 SAH sing 311 n n 
CG HG2 SAH sing 312 n n 
SD C5' SAH sing 313 n n 
C O SAH doub 314 n n 
C OXT SAH sing 315 n n 
OXT HXT SAH sing 316 n n 
C5' C4' SAH sing 317 n n 
C5' "H5'1" SAH sing 318 n n 
C5' "H5'2" SAH sing 319 n n 
C4' O4' SAH sing 320 n n 
C4' C3' SAH sing 321 n n 
C4' H4' SAH sing 322 n n 
O4' C1' SAH sing 323 n n 
C3' O3' SAH sing 324 n n 
C3' C2' SAH sing 325 n n 
C3' H3' SAH sing 326 n n 
O3' HO3' SAH sing 327 n n 
C2' O2' SAH sing 328 n n 
C2' C1' SAH sing 329 n n 
C2' H2' SAH sing 330 n n 
O2' HO2' SAH sing 331 n n 
C1' N9 SAH sing 332 n n 
C1' H1' SAH sing 333 n n 
N9 C8 SAH sing 334 n y 
N9 C4 SAH sing 335 n y 
C8 N7 SAH doub 336 n y 
C8 H8 SAH sing 337 n n 
N7 C5 SAH sing 338 n y 
C5 C6 SAH sing 339 n y 
C5 C4 SAH doub 340 n y 
C6 N6 SAH sing 341 n n 
C6 N1 SAH doub 342 n y 
N6 HN61 SAH sing 343 n n 
N6 HN62 SAH sing 344 n n 
N1 C2 SAH sing 345 n y 
C2 N3 SAH doub 346 n y 
C2 H2 SAH sing 347 n n 
N3 C4 SAH sing 348 n y 
#
_atom_sites.entry_id                     7U5V 
_atom_sites.fract_transf_matrix[1][1]    0.018355 
_atom_sites.fract_transf_matrix[1][2]    0.010597 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021195 
_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]    0.009467 
_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 3 ZN A 1 4001 4001 ZN ZN . 
D 4 SAH A 1 4002 4003 SAH SAH . 
#
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 4 -16.349 14.337 4.894 1 53.64 ? N SAH 4002 A 1 
HETATM 2 C CA SAH . . . D 4 -17.374 14.64 3.912 1 51.21 ? CA SAH 4002 A 1 
HETATM 3 C CB SAH . . . D 4 -18.399 15.592 4.528 1 56.89 ? CB SAH 4002 A 1 
HETATM 4 C CG SAH . . . D 4 -19.516 14.966 5.348 1 54.39 ? CG SAH 4002 A 1 
HETATM 5 S SD SAH . . . D 4 -20.828 14.435 4.23 1 50.36 ? SD SAH 4002 A 1 
HETATM 6 C C SAH . . . D 4 -16.778 15.245 2.633 1 48.75 ? C SAH 4002 A 1 
HETATM 7 O O SAH . . . D 4 -15.573 15.385 2.459 1 49.75 ? O SAH 4002 A 1 
HETATM 8 O OXT SAH . . . D 4 -17.492 15.623 1.709 1 54.64 ? OXT SAH 4002 A 1 
HETATM 9 C C5' SAH . . . D 4 -21.307 12.968 5.192 1 68.35 ? C5' SAH 4002 A 1 
HETATM 10 C C4' SAH . . . D 4 -20.602 11.726 4.674 1 67.75 ? C4' SAH 4002 A 1 
HETATM 11 O O4' SAH . . . D 4 -19.26 11.776 5.133 1 64.78 ? O4' SAH 4002 A 1 
HETATM 12 C C3' SAH . . . D 4 -21.186 10.398 5.138 1 74.86 ? C3' SAH 4002 A 1 
HETATM 13 O O3' SAH . . . D 4 -22.015 9.794 4.161 1 85.25 ? O3' SAH 4002 A 1 
HETATM 14 C C2' SAH . . . D 4 -19.944 9.563 5.349 1 64.12 ? C2' SAH 4002 A 1 
HETATM 15 O O2' SAH . . . D 4 -19.556 9.123 4.087 1 70.41 ? O2' SAH 4002 A 1 
HETATM 16 C C1' SAH . . . D 4 -18.864 10.546 5.713 1 66.07 ? C1' SAH 4002 A 1 
HETATM 17 N N9 SAH . . . D 4 -18.778 10.742 7.176 1 66.46 ? N9 SAH 4002 A 1 
HETATM 18 C C8 SAH . . . D 4 -19.292 11.83 7.84 1 63 ? C8 SAH 4002 A 1 
HETATM 19 N N7 SAH . . . D 4 -19.054 11.685 9.161 1 63.11 ? N7 SAH 4002 A 1 
HETATM 20 C C5 SAH . . . D 4 -18.407 10.525 9.349 1 60.52 ? C5 SAH 4002 A 1 
HETATM 21 C C6 SAH . . . D 4 -17.924 9.94 10.51 1 66.19 ? C6 SAH 4002 A 1 
HETATM 22 N N6 SAH . . . D 4 -18.121 10.563 11.67 1 64.5 ? N6 SAH 4002 A 1 
HETATM 23 N N1 SAH . . . D 4 -17.254 8.725 10.437 1 62.49 ? N1 SAH 4002 A 1 
HETATM 24 C C2 SAH . . . D 4 -17.081 8.124 9.196 1 60.32 ? C2 SAH 4002 A 1 
HETATM 25 N N3 SAH . . . D 4 -17.559 8.733 8.039 1 62.79 ? N3 SAH 4002 A 1 
HETATM 26 C C4 SAH . . . D 4 -18.215 9.915 8.114 1 59.19 ? C4 SAH 4002 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           258 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#