data_4PYO
#
_model_server_result.job_id            1ZJrO6IBt3X8biL5QKdCQA 
_model_server_result.datetime_utc      '2024-11-04 22:51:06' 
_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          4pyo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":301}' 
#
_entry.id    4PYO 
#
_exptl.entry_id    4PYO 
_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            4PYO 
_cell.length_a            58.369 
_cell.length_b            60.38 
_cell.length_c            148.415 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PYO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 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
metalc ? metalc1 A O VAL 183 A VAL 226 1_555 D K K . A K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? 
metalc ? metalc2 A O ARG 184 A ARG 227 1_555 D K K . A K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? 
metalc ? metalc3 A O SER 186 A SER 229 1_555 D K K . A K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? 
metalc ? metalc4 A O PHE 189 A PHE 232 1_555 D K K . A K 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? 
metalc ? metalc5 D K K . A K 302 1_555 G O HOH . A HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.698 ? 
metalc ? metalc6 D K K . A K 302 1_555 G O HOH . A HOH 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? 
metalc ? metalc7 B OD1 ASP 141 B ASP 184 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc8 B OD2 ASP 169 B ASP 212 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc9 B OD1 ASN 170 B ASN 213 1_555 F MG MG . B MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc10 F MG MG . B MG 302 1_555 H O HOH . B HOH 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
metalc ? metalc11 F MG MG . B MG 302 1_555 H O HOH . B HOH 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc12 F MG MG . B MG 302 1_555 H O HOH . B HOH 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
#
_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                     4PYO 
_atom_sites.fract_transf_matrix[1][1]    0.017132 
_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]    0.016562 
_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]    0.006738 
_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 1 301 301 SAH SAH . 
D 3 K A 1 302 353 K K . 
E 2 SAH B 1 301 301 SAH SAH . 
F 4 MG B 1 302 363 MG MG . 
G 5 HOH A 1 401 1 HOH HOH . 
G 5 HOH A 2 402 4 HOH HOH . 
G 5 HOH A 3 403 6 HOH HOH . 
G 5 HOH A 4 404 8 HOH HOH . 
G 5 HOH A 5 405 12 HOH HOH . 
G 5 HOH A 6 406 13 HOH HOH . 
G 5 HOH A 7 407 16 HOH HOH . 
G 5 HOH A 8 408 17 HOH HOH . 
G 5 HOH A 9 409 18 HOH HOH . 
G 5 HOH A 10 410 19 HOH HOH . 
G 5 HOH A 11 411 21 HOH HOH . 
G 5 HOH A 12 412 23 HOH HOH . 
G 5 HOH A 13 413 24 HOH HOH . 
G 5 HOH A 14 414 25 HOH HOH . 
G 5 HOH A 15 415 27 HOH HOH . 
G 5 HOH A 16 416 29 HOH HOH . 
G 5 HOH A 17 417 30 HOH HOH . 
G 5 HOH A 18 418 31 HOH HOH . 
G 5 HOH A 19 419 32 HOH HOH . 
G 5 HOH A 20 420 33 HOH HOH . 
G 5 HOH A 21 421 34 HOH HOH . 
G 5 HOH A 22 422 36 HOH HOH . 
G 5 HOH A 23 423 39 HOH HOH . 
G 5 HOH A 24 424 42 HOH HOH . 
G 5 HOH A 25 425 43 HOH HOH . 
G 5 HOH A 26 426 44 HOH HOH . 
G 5 HOH A 27 427 46 HOH HOH . 
G 5 HOH A 28 428 47 HOH HOH . 
G 5 HOH A 29 429 48 HOH HOH . 
G 5 HOH A 30 430 49 HOH HOH . 
G 5 HOH A 31 431 53 HOH HOH . 
G 5 HOH A 32 432 55 HOH HOH . 
G 5 HOH A 33 433 56 HOH HOH . 
G 5 HOH A 34 434 57 HOH HOH . 
G 5 HOH A 35 435 61 HOH HOH . 
G 5 HOH A 36 436 63 HOH HOH . 
G 5 HOH A 37 437 64 HOH HOH . 
G 5 HOH A 38 438 65 HOH HOH . 
G 5 HOH A 39 439 66 HOH HOH . 
G 5 HOH A 40 440 67 HOH HOH . 
G 5 HOH A 41 441 70 HOH HOH . 
G 5 HOH A 42 442 72 HOH HOH . 
G 5 HOH A 43 443 73 HOH HOH . 
G 5 HOH A 44 444 74 HOH HOH . 
G 5 HOH A 45 445 77 HOH HOH . 
G 5 HOH A 46 446 78 HOH HOH . 
G 5 HOH A 47 447 80 HOH HOH . 
G 5 HOH A 48 448 82 HOH HOH . 
G 5 HOH A 49 449 83 HOH HOH . 
G 5 HOH A 50 450 84 HOH HOH . 
G 5 HOH A 51 451 85 HOH HOH . 
G 5 HOH A 52 452 87 HOH HOH . 
G 5 HOH A 53 453 88 HOH HOH . 
G 5 HOH A 54 454 90 HOH HOH . 
G 5 HOH A 55 455 93 HOH HOH . 
G 5 HOH A 56 456 96 HOH HOH . 
G 5 HOH A 57 457 100 HOH HOH . 
G 5 HOH A 58 458 102 HOH HOH . 
G 5 HOH A 59 459 104 HOH HOH . 
G 5 HOH A 60 460 106 HOH HOH . 
G 5 HOH A 61 461 109 HOH HOH . 
G 5 HOH A 62 462 110 HOH HOH . 
H 5 HOH B 1 401 2 HOH HOH . 
H 5 HOH B 2 402 3 HOH HOH . 
H 5 HOH B 3 403 7 HOH HOH . 
H 5 HOH B 4 404 9 HOH HOH . 
H 5 HOH B 5 405 10 HOH HOH . 
H 5 HOH B 6 406 11 HOH HOH . 
H 5 HOH B 7 407 14 HOH HOH . 
H 5 HOH B 8 408 15 HOH HOH . 
H 5 HOH B 9 409 20 HOH HOH . 
H 5 HOH B 10 410 22 HOH HOH . 
H 5 HOH B 11 411 26 HOH HOH . 
H 5 HOH B 12 412 28 HOH HOH . 
H 5 HOH B 13 413 35 HOH HOH . 
H 5 HOH B 14 414 37 HOH HOH . 
H 5 HOH B 15 415 38 HOH HOH . 
H 5 HOH B 16 416 40 HOH HOH . 
H 5 HOH B 17 417 41 HOH HOH . 
H 5 HOH B 18 418 45 HOH HOH . 
H 5 HOH B 19 419 50 HOH HOH . 
H 5 HOH B 20 420 51 HOH HOH . 
H 5 HOH B 21 421 52 HOH HOH . 
H 5 HOH B 22 422 54 HOH HOH . 
H 5 HOH B 23 423 58 HOH HOH . 
H 5 HOH B 24 424 59 HOH HOH . 
H 5 HOH B 25 425 60 HOH HOH . 
H 5 HOH B 26 426 62 HOH HOH . 
H 5 HOH B 27 427 68 HOH HOH . 
H 5 HOH B 28 428 69 HOH HOH . 
H 5 HOH B 29 429 71 HOH HOH . 
H 5 HOH B 30 430 75 HOH HOH . 
H 5 HOH B 31 431 76 HOH HOH . 
H 5 HOH B 32 432 79 HOH HOH . 
H 5 HOH B 33 433 81 HOH HOH . 
H 5 HOH B 34 434 86 HOH HOH . 
H 5 HOH B 35 435 89 HOH HOH . 
H 5 HOH B 36 436 91 HOH HOH . 
H 5 HOH B 37 437 92 HOH HOH . 
H 5 HOH B 38 438 94 HOH HOH . 
H 5 HOH B 39 439 95 HOH HOH . 
H 5 HOH B 40 440 97 HOH HOH . 
H 5 HOH B 41 441 98 HOH HOH . 
H 5 HOH B 42 442 99 HOH HOH . 
H 5 HOH B 43 443 101 HOH HOH . 
H 5 HOH B 44 444 103 HOH HOH . 
H 5 HOH B 45 445 105 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 . . . C 2 10.597 0.584 -31.759 1 42.26 ? N SAH 301 A 1 
HETATM 2 C CA SAH . . . C 2 11.65 1.337 -32.404 1 49.23 ? CA SAH 301 A 1 
HETATM 3 C CB SAH . . . C 2 11.138 2.02 -33.666 1 40.53 ? CB SAH 301 A 1 
HETATM 4 C CG SAH . . . C 2 10.449 1.06 -34.624 1 37.47 ? CG SAH 301 A 1 
HETATM 5 S SD SAH . . . C 2 10.277 1.77 -36.225 1 39.78 ? SD SAH 301 A 1 
HETATM 6 C C SAH . . . C 2 12.145 2.384 -31.455 1 60.49 ? C SAH 301 A 1 
HETATM 7 O O SAH . . . C 2 11.417 2.716 -30.503 1 64.06 ? O SAH 301 A 1 
HETATM 8 O OXT SAH . . . C 2 13.262 2.892 -31.653 1 64.58 -1 OXT SAH 301 A 1 
HETATM 9 C C5' SAH . . . C 2 9.501 0.409 -37.019 1 33.54 ? C5' SAH 301 A 1 
HETATM 10 C C4' SAH . . . C 2 10.544 -0.604 -37.47 1 33.08 ? C4' SAH 301 A 1 
HETATM 11 O O4' SAH . . . C 2 9.931 -1.856 -37.726 1 36.53 ? O4' SAH 301 A 1 
HETATM 12 C C3' SAH . . . C 2 11.247 -0.204 -38.749 1 33.84 ? C3' SAH 301 A 1 
HETATM 13 O O3' SAH . . . C 2 12.639 -0.271 -38.494 1 31.68 ? O3' SAH 301 A 1 
HETATM 14 C C2' SAH . . . C 2 10.851 -1.246 -39.774 1 35.22 ? C2' SAH 301 A 1 
HETATM 15 O O2' SAH . . . C 2 11.947 -1.597 -40.603 1 30.17 ? O2' SAH 301 A 1 
HETATM 16 C C1' SAH . . . C 2 10.44 -2.422 -38.917 1 35.37 ? C1' SAH 301 A 1 
HETATM 17 N N9 SAH . . . C 2 9.378 -3.255 -39.508 1 37.78 ? N9 SAH 301 A 1 
HETATM 18 C C8 SAH . . . C 2 8.33 -2.85 -40.223 1 37.69 ? C8 SAH 301 A 1 
HETATM 19 N N7 SAH . . . C 2 7.561 -3.892 -40.583 1 36.69 ? N7 SAH 301 A 1 
HETATM 20 C C5 SAH . . . C 2 8.121 -4.998 -40.089 1 35.53 ? C5 SAH 301 A 1 
HETATM 21 C C6 SAH . . . C 2 7.831 -6.444 -40.09 1 32.86 ? C6 SAH 301 A 1 
HETATM 22 N N6 SAH . . . C 2 6.757 -6.95 -40.712 1 27.54 ? N6 SAH 301 A 1 
HETATM 23 N N1 SAH . . . C 2 8.683 -7.25 -39.45 1 34.94 ? N1 SAH 301 A 1 
HETATM 24 C C2 SAH . . . C 2 9.76 -6.779 -38.826 1 31.19 ? C2 SAH 301 A 1 
HETATM 25 N N3 SAH . . . C 2 10.077 -5.487 -38.78 1 35.1 ? N3 SAH 301 A 1 
HETATM 26 C C4 SAH . . . C 2 9.317 -4.566 -39.382 1 34.46 ? C4 SAH 301 A 1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#