data_6P7D
#
_model_server_result.job_id            i87846gq5tRiddVbWqUY8Q 
_model_server_result.datetime_utc      '2025-03-30 06:30:44' 
_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          6p7d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":501}' 
#
_entry.id    6P7D 
#
_exptl.entry_id    6P7D 
_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            6P7D 
_cell.length_a            60.096 
_cell.length_b            99.329 
_cell.length_c            147.421 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6P7D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_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 
_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 D N N 
#
_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                     6P7D 
_atom_sites.fract_transf_matrix[1][1]    0.01664 
_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]    0.010068 
_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]    0.006783 
_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 1 501 501 SAH SAH . 
D 2 SAH B 1 501 502 SAH SAH . 
E 3 CL B 1 502 1 CL CL . 
F 4 HOH A 1 601 82 HOH HOH . 
F 4 HOH A 2 602 49 HOH HOH . 
F 4 HOH A 3 603 16 HOH HOH . 
F 4 HOH A 4 604 23 HOH HOH . 
F 4 HOH A 5 605 80 HOH HOH . 
F 4 HOH A 6 606 36 HOH HOH . 
F 4 HOH A 7 607 50 HOH HOH . 
F 4 HOH A 8 608 76 HOH HOH . 
F 4 HOH A 9 609 94 HOH HOH . 
F 4 HOH A 10 610 84 HOH HOH . 
F 4 HOH A 11 611 63 HOH HOH . 
F 4 HOH A 12 612 40 HOH HOH . 
F 4 HOH A 13 613 77 HOH HOH . 
F 4 HOH A 14 614 102 HOH HOH . 
F 4 HOH A 15 615 6 HOH HOH . 
F 4 HOH A 16 616 92 HOH HOH . 
F 4 HOH A 17 617 4 HOH HOH . 
F 4 HOH A 18 618 21 HOH HOH . 
F 4 HOH A 19 619 29 HOH HOH . 
F 4 HOH A 20 620 11 HOH HOH . 
F 4 HOH A 21 621 97 HOH HOH . 
F 4 HOH A 22 622 75 HOH HOH . 
F 4 HOH A 23 623 13 HOH HOH . 
F 4 HOH A 24 624 66 HOH HOH . 
F 4 HOH A 25 625 105 HOH HOH . 
F 4 HOH A 26 626 32 HOH HOH . 
F 4 HOH A 27 627 39 HOH HOH . 
F 4 HOH A 28 628 15 HOH HOH . 
F 4 HOH A 29 629 46 HOH HOH . 
F 4 HOH A 30 630 64 HOH HOH . 
F 4 HOH A 31 631 35 HOH HOH . 
F 4 HOH A 32 632 68 HOH HOH . 
F 4 HOH A 33 633 112 HOH HOH . 
F 4 HOH A 34 634 19 HOH HOH . 
F 4 HOH A 35 635 26 HOH HOH . 
F 4 HOH A 36 636 12 HOH HOH . 
F 4 HOH A 37 637 37 HOH HOH . 
F 4 HOH A 38 638 96 HOH HOH . 
F 4 HOH A 39 639 81 HOH HOH . 
F 4 HOH A 40 640 47 HOH HOH . 
F 4 HOH A 41 641 25 HOH HOH . 
F 4 HOH A 42 642 86 HOH HOH . 
F 4 HOH A 43 643 31 HOH HOH . 
F 4 HOH A 44 644 8 HOH HOH . 
F 4 HOH A 45 645 9 HOH HOH . 
F 4 HOH A 46 646 17 HOH HOH . 
F 4 HOH A 47 647 34 HOH HOH . 
F 4 HOH A 48 648 62 HOH HOH . 
F 4 HOH A 49 649 101 HOH HOH . 
F 4 HOH A 50 650 33 HOH HOH . 
F 4 HOH A 51 651 38 HOH HOH . 
F 4 HOH A 52 652 58 HOH HOH . 
F 4 HOH A 53 653 51 HOH HOH . 
F 4 HOH A 54 654 72 HOH HOH . 
F 4 HOH A 55 655 45 HOH HOH . 
F 4 HOH A 56 656 28 HOH HOH . 
F 4 HOH A 57 657 60 HOH HOH . 
F 4 HOH A 58 658 70 HOH HOH . 
F 4 HOH A 59 659 56 HOH HOH . 
F 4 HOH A 60 660 57 HOH HOH . 
F 4 HOH A 61 661 52 HOH HOH . 
F 4 HOH A 62 662 71 HOH HOH . 
F 4 HOH A 63 663 99 HOH HOH . 
F 4 HOH A 64 664 74 HOH HOH . 
F 4 HOH A 65 665 91 HOH HOH . 
F 4 HOH A 66 666 73 HOH HOH . 
F 4 HOH A 67 667 61 HOH HOH . 
F 4 HOH A 68 668 78 HOH HOH . 
G 4 HOH B 1 601 54 HOH HOH . 
G 4 HOH B 2 602 79 HOH HOH . 
G 4 HOH B 3 603 107 HOH HOH . 
G 4 HOH B 4 604 55 HOH HOH . 
G 4 HOH B 5 605 5 HOH HOH . 
G 4 HOH B 6 606 83 HOH HOH . 
G 4 HOH B 7 607 2 HOH HOH . 
G 4 HOH B 8 608 109 HOH HOH . 
G 4 HOH B 9 609 106 HOH HOH . 
G 4 HOH B 10 610 103 HOH HOH . 
G 4 HOH B 11 611 43 HOH HOH . 
G 4 HOH B 12 612 27 HOH HOH . 
G 4 HOH B 13 613 18 HOH HOH . 
G 4 HOH B 14 614 30 HOH HOH . 
G 4 HOH B 15 615 65 HOH HOH . 
G 4 HOH B 16 616 110 HOH HOH . 
G 4 HOH B 17 617 44 HOH HOH . 
G 4 HOH B 18 618 1 HOH HOH . 
G 4 HOH B 19 619 87 HOH HOH . 
G 4 HOH B 20 620 67 HOH HOH . 
G 4 HOH B 21 621 24 HOH HOH . 
G 4 HOH B 22 622 42 HOH HOH . 
G 4 HOH B 23 623 3 HOH HOH . 
G 4 HOH B 24 624 69 HOH HOH . 
G 4 HOH B 25 625 100 HOH HOH . 
G 4 HOH B 26 626 88 HOH HOH . 
G 4 HOH B 27 627 89 HOH HOH . 
G 4 HOH B 28 628 85 HOH HOH . 
G 4 HOH B 29 629 10 HOH HOH . 
G 4 HOH B 30 630 20 HOH HOH . 
G 4 HOH B 31 631 7 HOH HOH . 
G 4 HOH B 32 632 104 HOH HOH . 
G 4 HOH B 33 633 95 HOH HOH . 
G 4 HOH B 34 634 14 HOH HOH . 
G 4 HOH B 35 635 53 HOH HOH . 
G 4 HOH B 36 636 59 HOH HOH . 
G 4 HOH B 37 637 22 HOH HOH . 
G 4 HOH B 38 638 41 HOH HOH . 
G 4 HOH B 39 639 98 HOH HOH . 
G 4 HOH B 40 640 48 HOH HOH . 
G 4 HOH B 41 641 90 HOH HOH . 
G 4 HOH B 42 642 111 HOH HOH . 
G 4 HOH B 43 643 93 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 2 46.897 -15.601 13.075 1 62.93 ? N SAH 501 B 1 
HETATM 2 C CA SAH . . . D 2 48.021 -14.955 13.739 1 62.01 ? CA SAH 501 B 1 
HETATM 3 C CB SAH . . . D 2 49.244 -14.922 12.808 1 58.93 ? CB SAH 501 B 1 
HETATM 4 C CG SAH . . . D 2 50.015 -16.224 12.621 1 55.88 ? CG SAH 501 B 1 
HETATM 5 S SD SAH . . . D 2 51.597 -15.983 11.746 1 63.61 ? SD SAH 501 B 1 
HETATM 6 C C SAH . . . D 2 47.661 -13.532 14.206 1 59.71 ? C SAH 501 B 1 
HETATM 7 O O SAH . . . D 2 46.713 -12.905 13.747 1 50.72 ? O SAH 501 B 1 
HETATM 8 O OXT SAH . . . D 2 48.323 -12.945 15.057 1 59.92 ? OXT SAH 501 B 1 
HETATM 9 C C5' SAH . . . D 2 52.665 -16.29 13.192 1 64.38 ? C5' SAH 501 B 1 
HETATM 10 C C4' SAH . . . D 2 53.501 -15.066 13.583 1 62.78 ? C4' SAH 501 B 1 
HETATM 11 O O4' SAH . . . D 2 52.77 -14.077 14.32 1 57.7 ? O4' SAH 501 B 1 
HETATM 12 C C3' SAH . . . D 2 54.723 -15.393 14.429 1 58.46 ? C3' SAH 501 B 1 
HETATM 13 O O3' SAH . . . D 2 55.811 -15.813 13.649 1 63.16 ? O3' SAH 501 B 1 
HETATM 14 C C2' SAH . . . D 2 55.012 -14.066 15.105 1 58.54 ? C2' SAH 501 B 1 
HETATM 15 O O2' SAH . . . D 2 55.738 -13.186 14.268 1 53.68 ? O2' SAH 501 B 1 
HETATM 16 C C1' SAH . . . D 2 53.629 -13.47 15.273 1 57.26 ? C1' SAH 501 B 1 
HETATM 17 N N9 SAH . . . D 2 53.1 -13.708 16.631 1 45.57 ? N9 SAH 501 B 1 
HETATM 18 C C8 SAH . . . D 2 52.083 -14.565 16.944 1 40.42 ? C8 SAH 501 B 1 
HETATM 19 N N7 SAH . . . D 2 51.866 -14.519 18.266 1 38.01 ? N7 SAH 501 B 1 
HETATM 20 C C5 SAH . . . D 2 52.729 -13.647 18.832 1 44.41 ? C5 SAH 501 B 1 
HETATM 21 C C6 SAH . . . D 2 52.929 -13.213 20.153 1 49.74 ? C6 SAH 501 B 1 
HETATM 22 N N6 SAH . . . D 2 52.197 -13.671 21.176 1 49.51 ? N6 SAH 501 B 1 
HETATM 23 N N1 SAH . . . D 2 53.919 -12.278 20.398 1 56.26 ? N1 SAH 501 B 1 
HETATM 24 C C2 SAH . . . D 2 54.681 -11.777 19.365 1 48.54 ? C2 SAH 501 B 1 
HETATM 25 N N3 SAH . . . D 2 54.469 -12.216 18.069 1 43.26 ? N3 SAH 501 B 1 
HETATM 26 C C4 SAH . . . D 2 53.517 -13.133 17.8 1 43.89 ? C4 SAH 501 B 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    45 
_model_server_stats.query_time_ms           548 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#