data_3RIB
#
_model_server_result.job_id            CsP7G4y7rfI2IXJevX4Iaw 
_model_server_result.datetime_utc      '2024-11-09 02:02:17' 
_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          3rib 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":445}' 
#
_entry.id    3RIB 
#
_exptl.entry_id    3RIB 
_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          103.95 
_cell.angle_gamma         90 
_cell.entry_id            3RIB 
_cell.length_a            194.56 
_cell.length_b            57.185 
_cell.length_c            96.607 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3RIB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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,E,F,G,H,I,J,K,L,M,T 1 1 
B,N,O,P,Q,R,S,U 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
? 3 F N N 
? 3 Q 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 SG CYS 52 A CYS 52 1_555 C ZN ZN . A ZN 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? 
metalc ? metalc2 A SG CYS 55 A CYS 55 1_555 C ZN ZN . A ZN 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc3 A SG CYS 65 A CYS 65 1_555 D ZN ZN . A ZN 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? 
metalc ? metalc4 A SG CYS 68 A CYS 68 1_555 D ZN ZN . A ZN 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? 
metalc ? metalc5 A SG CYS 74 A CYS 74 1_555 C ZN ZN . A ZN 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc6 A SG CYS 78 A CYS 78 1_555 C ZN ZN . A ZN 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? 
metalc ? metalc7 A NE2 HIS 86 A HIS 86 1_555 D ZN ZN . A ZN 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? 
metalc ? metalc8 A SG CYS 90 A CYS 90 1_555 D ZN ZN . A ZN 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? 
metalc ? metalc9 A SG CYS 209 A CYS 209 1_555 E ZN ZN . A ZN 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc10 A SG CYS 262 A CYS 262 1_555 E ZN ZN . A ZN 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc11 A SG CYS 264 A CYS 264 1_555 E ZN ZN . A ZN 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? 
metalc ? metalc12 A SG CYS 267 A CYS 267 1_555 E ZN ZN . A ZN 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? 
metalc ? metalc13 B SG CYS 52 B CYS 52 1_555 N ZN ZN . B ZN 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? 
metalc ? metalc14 B SG CYS 55 B CYS 55 1_555 N ZN ZN . B ZN 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? 
metalc ? metalc15 B SG CYS 65 B CYS 65 1_555 O ZN ZN . B ZN 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc16 B SG CYS 68 B CYS 68 1_555 O ZN ZN . B ZN 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc17 B SG CYS 74 B CYS 74 1_555 N ZN ZN . B ZN 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
metalc ? metalc18 B SG CYS 78 B CYS 78 1_555 N ZN ZN . B ZN 442 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? 
metalc ? metalc19 B NE2 HIS 86 B HIS 86 1_555 O ZN ZN . B ZN 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? 
metalc ? metalc20 B SG CYS 90 B CYS 90 1_555 O ZN ZN . B ZN 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc21 B SG CYS 209 B CYS 209 1_555 P ZN ZN . B ZN 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.493 ? 
metalc ? metalc22 B SG CYS 262 B CYS 262 1_555 P ZN ZN . B ZN 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc23 B SG CYS 264 B CYS 264 1_555 P ZN ZN . B ZN 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.85 ? 
metalc ? metalc24 B SG CYS 267 B CYS 267 1_555 P ZN ZN . B ZN 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
#
_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                     3RIB 
_atom_sites.fract_transf_matrix[1][1]    0.00514 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001277 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.017487 
_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]    0.010666 
_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 ZN A 1 442 4 ZN ZN . 
D 2 ZN A 1 443 5 ZN ZN . 
E 2 ZN A 1 444 6 ZN ZN . 
F 3 SAH A 1 445 100 SAH SAH . 
G 4 SO4 A 1 446 2 SO4 SO4 . 
H 4 SO4 A 1 447 4 SO4 SO4 . 
I 4 SO4 A 1 448 5 SO4 SO4 . 
J 4 SO4 A 1 449 6 SO4 SO4 . 
K 4 SO4 A 1 450 7 SO4 SO4 . 
L 4 SO4 A 1 451 9 SO4 SO4 . 
M 4 SO4 A 1 452 10 SO4 SO4 . 
N 2 ZN B 1 442 1 ZN ZN . 
O 2 ZN B 1 443 2 ZN ZN . 
P 2 ZN B 1 444 3 ZN ZN . 
Q 3 SAH B 1 445 100 SAH SAH . 
R 4 SO4 B 1 446 1 SO4 SO4 . 
S 4 SO4 B 1 447 3 SO4 SO4 . 
T 5 HOH A 1 453 10 HOH HOH . 
T 5 HOH A 2 454 12 HOH HOH . 
T 5 HOH A 3 455 13 HOH HOH . 
T 5 HOH A 4 456 14 HOH HOH . 
T 5 HOH A 5 457 15 HOH HOH . 
T 5 HOH A 6 458 16 HOH HOH . 
T 5 HOH A 7 459 17 HOH HOH . 
T 5 HOH A 8 460 18 HOH HOH . 
T 5 HOH A 9 461 19 HOH HOH . 
T 5 HOH A 10 462 20 HOH HOH . 
T 5 HOH A 11 463 22 HOH HOH . 
T 5 HOH A 12 464 23 HOH HOH . 
T 5 HOH A 13 465 24 HOH HOH . 
T 5 HOH A 14 466 25 HOH HOH . 
T 5 HOH A 15 467 26 HOH HOH . 
T 5 HOH A 16 468 27 HOH HOH . 
T 5 HOH A 17 469 28 HOH HOH . 
T 5 HOH A 18 470 30 HOH HOH . 
T 5 HOH A 19 471 31 HOH HOH . 
T 5 HOH A 20 472 32 HOH HOH . 
T 5 HOH A 21 473 33 HOH HOH . 
T 5 HOH A 22 474 35 HOH HOH . 
T 5 HOH A 23 475 36 HOH HOH . 
T 5 HOH A 24 476 37 HOH HOH . 
T 5 HOH A 25 477 38 HOH HOH . 
T 5 HOH A 26 478 39 HOH HOH . 
T 5 HOH A 27 479 40 HOH HOH . 
T 5 HOH A 28 480 41 HOH HOH . 
T 5 HOH A 29 481 42 HOH HOH . 
T 5 HOH A 30 482 43 HOH HOH . 
T 5 HOH A 31 483 44 HOH HOH . 
T 5 HOH A 32 484 45 HOH HOH . 
T 5 HOH A 33 485 46 HOH HOH . 
T 5 HOH A 34 486 49 HOH HOH . 
T 5 HOH A 35 487 3 HOH HOH . 
T 5 HOH A 36 488 4 HOH HOH . 
T 5 HOH A 37 489 5 HOH HOH . 
T 5 HOH A 38 490 6 HOH HOH . 
T 5 HOH A 39 491 9 HOH HOH . 
U 5 HOH B 1 448 8 HOH HOH . 
U 5 HOH B 2 449 11 HOH HOH . 
U 5 HOH B 3 450 21 HOH HOH . 
U 5 HOH B 4 451 29 HOH HOH . 
U 5 HOH B 5 452 34 HOH HOH . 
U 5 HOH B 6 453 47 HOH HOH . 
U 5 HOH B 7 454 48 HOH HOH . 
U 5 HOH B 8 455 1 HOH HOH . 
U 5 HOH B 9 456 2 HOH HOH . 
U 5 HOH B 10 457 7 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 . . . F 3 8.46 -22.493 -11.045 1 32.46 ? N SAH 445 A 1 
HETATM 2 C CA SAH . . . F 3 8.668 -22.392 -9.569 1 32.43 ? CA SAH 445 A 1 
HETATM 3 C CB SAH . . . F 3 10.001 -21.704 -9.276 1 32.32 ? CB SAH 445 A 1 
HETATM 4 C CG SAH . . . F 3 11.156 -22.696 -9.398 1 31.8 ? CG SAH 445 A 1 
HETATM 5 S SD SAH . . . F 3 11.235 -23.728 -7.969 1 30.67 ? SD SAH 445 A 1 
HETATM 6 C C SAH . . . F 3 7.517 -21.664 -8.936 1 32.58 ? C SAH 445 A 1 
HETATM 7 O O SAH . . . F 3 6.474 -21.471 -9.568 1 32.62 ? O SAH 445 A 1 
HETATM 8 O OXT SAH . . . F 3 7.574 -21.257 -7.771 1 32.61 ? OXT SAH 445 A 1 
HETATM 9 C C5' SAH . . . F 3 11.324 -25.339 -8.699 1 30.14 ? C5' SAH 445 A 1 
HETATM 10 C C4' SAH . . . F 3 9.955 -25.89 -9.106 1 29.06 ? C4' SAH 445 A 1 
HETATM 11 O O4' SAH . . . F 3 9.564 -25.37 -10.384 1 28.35 ? O4' SAH 445 A 1 
HETATM 12 C C3' SAH . . . F 3 9.967 -27.407 -9.259 1 28.78 ? C3' SAH 445 A 1 
HETATM 13 O O3' SAH . . . F 3 9.487 -28.07 -8.084 1 28.42 ? O3' SAH 445 A 1 
HETATM 14 C C2' SAH . . . F 3 9.087 -27.691 -10.466 1 28.49 ? C2' SAH 445 A 1 
HETATM 15 O O2' SAH . . . F 3 7.731 -27.95 -10.093 1 28.58 ? O2' SAH 445 A 1 
HETATM 16 C C1' SAH . . . F 3 9.119 -26.406 -11.271 1 28.12 ? C1' SAH 445 A 1 
HETATM 17 N N9 SAH . . . F 3 10.056 -26.563 -12.416 1 27.58 ? N9 SAH 445 A 1 
HETATM 18 C C8 SAH . . . F 3 11.342 -26.155 -12.447 1 27.25 ? C8 SAH 445 A 1 
HETATM 19 N N7 SAH . . . F 3 11.928 -26.441 -13.636 1 26.87 ? N7 SAH 445 A 1 
HETATM 20 C C5 SAH . . . F 3 11.004 -27.052 -14.398 1 26.99 ? C5 SAH 445 A 1 
HETATM 21 C C6 SAH . . . F 3 10.954 -27.618 -15.768 1 26.42 ? C6 SAH 445 A 1 
HETATM 22 N N6 SAH . . . F 3 12.044 -27.585 -16.566 1 26.21 ? N6 SAH 445 A 1 
HETATM 23 N N1 SAH . . . F 3 9.791 -28.171 -16.186 1 26.36 ? N1 SAH 445 A 1 
HETATM 24 C C2 SAH . . . F 3 8.699 -28.212 -15.394 1 26.43 ? C2 SAH 445 A 1 
HETATM 25 N N3 SAH . . . F 3 8.671 -27.718 -14.14 1 26.78 ? N3 SAH 445 A 1 
HETATM 26 C C4 SAH . . . F 3 9.77 -27.134 -13.592 1 27.27 ? C4 SAH 445 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           247 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#