data_6KDP
#
_model_server_result.job_id            VWykjHPmA0NPR3Om4BEnog 
_model_server_result.datetime_utc      '2024-10-10 05:23:46' 
_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          6kdp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":902}' 
#
_entry.id    6KDP 
#
_exptl.entry_id    6KDP 
_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    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            6KDP 
_cell.length_a            72.105 
_cell.length_b            234.066 
_cell.length_c            230.951 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6KDP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L 
_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
? 4 F N N 
? 4 H 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 281 n n 
N HN1 SAH sing 282 n n 
N HN2 SAH sing 283 n n 
CA CB SAH sing 284 n n 
CA C SAH sing 285 n n 
CA HA SAH sing 286 n n 
CB CG SAH sing 287 n n 
CB HB1 SAH sing 288 n n 
CB HB2 SAH sing 289 n n 
CG SD SAH sing 290 n n 
CG HG1 SAH sing 291 n n 
CG HG2 SAH sing 292 n n 
SD C5' SAH sing 293 n n 
C O SAH doub 294 n n 
C OXT SAH sing 295 n n 
OXT HXT SAH sing 296 n n 
C5' C4' SAH sing 297 n n 
C5' "H5'1" SAH sing 298 n n 
C5' "H5'2" SAH sing 299 n n 
C4' O4' SAH sing 300 n n 
C4' C3' SAH sing 301 n n 
C4' H4' SAH sing 302 n n 
O4' C1' SAH sing 303 n n 
C3' O3' SAH sing 304 n n 
C3' C2' SAH sing 305 n n 
C3' H3' SAH sing 306 n n 
O3' HO3' SAH sing 307 n n 
C2' O2' SAH sing 308 n n 
C2' C1' SAH sing 309 n n 
C2' H2' SAH sing 310 n n 
O2' HO2' SAH sing 311 n n 
C1' N9 SAH sing 312 n n 
C1' H1' SAH sing 313 n n 
N9 C8 SAH sing 314 n y 
N9 C4 SAH sing 315 n y 
C8 N7 SAH doub 316 n y 
C8 H8 SAH sing 317 n n 
N7 C5 SAH sing 318 n y 
C5 C6 SAH sing 319 n y 
C5 C4 SAH doub 320 n y 
C6 N6 SAH sing 321 n n 
C6 N1 SAH doub 322 n y 
N6 HN61 SAH sing 323 n n 
N6 HN62 SAH sing 324 n n 
N1 C2 SAH sing 325 n y 
C2 N3 SAH doub 326 n y 
C2 H2 SAH sing 327 n n 
N3 C4 SAH sing 328 n y 
#
_atom_sites.entry_id                     6KDP 
_atom_sites.fract_transf_matrix[1][1]    0.013869 
_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]    0.004272 
_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]    0.00433 
_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
E 3 FMT A 1 901 2 FMT FMT . 
F 4 SAH A 1 902 900 SAH SAH . 
G 3 FMT D 1 901 1 FMT FMT . 
H 4 SAH D 1 902 910 SAH SAH . 
I 5 HOH A 1 1001 68 HOH HOH . 
I 5 HOH A 2 1002 80 HOH HOH . 
I 5 HOH A 3 1003 100 HOH HOH . 
I 5 HOH A 4 1004 94 HOH HOH . 
I 5 HOH A 5 1005 101 HOH HOH . 
I 5 HOH A 6 1006 93 HOH HOH . 
I 5 HOH A 7 1007 111 HOH HOH . 
I 5 HOH A 8 1008 73 HOH HOH . 
I 5 HOH A 9 1009 75 HOH HOH . 
I 5 HOH A 10 1010 7 HOH HOH . 
I 5 HOH A 11 1011 88 HOH HOH . 
I 5 HOH A 12 1012 99 HOH HOH . 
I 5 HOH A 13 1013 95 HOH HOH . 
I 5 HOH A 14 1014 79 HOH HOH . 
I 5 HOH A 15 1015 76 HOH HOH . 
I 5 HOH A 16 1016 91 HOH HOH . 
I 5 HOH A 17 1017 84 HOH HOH . 
I 5 HOH A 18 1018 4 HOH HOH . 
I 5 HOH A 19 1019 64 HOH HOH . 
I 5 HOH A 20 1020 39 HOH HOH . 
I 5 HOH A 21 1021 82 HOH HOH . 
I 5 HOH A 22 1022 6 HOH HOH . 
I 5 HOH A 23 1023 70 HOH HOH . 
I 5 HOH A 24 1024 81 HOH HOH . 
I 5 HOH A 25 1025 96 HOH HOH . 
I 5 HOH A 26 1026 83 HOH HOH . 
I 5 HOH A 27 1027 92 HOH HOH . 
I 5 HOH A 28 1028 43 HOH HOH . 
I 5 HOH A 29 1029 112 HOH HOH . 
I 5 HOH A 30 1030 65 HOH HOH . 
I 5 HOH A 31 1031 69 HOH HOH . 
I 5 HOH A 32 1032 77 HOH HOH . 
I 5 HOH A 33 1033 90 HOH HOH . 
I 5 HOH A 34 1034 97 HOH HOH . 
I 5 HOH A 35 1035 85 HOH HOH . 
I 5 HOH A 36 1036 67 HOH HOH . 
I 5 HOH A 37 1037 78 HOH HOH . 
I 5 HOH A 38 1038 86 HOH HOH . 
I 5 HOH A 39 1039 102 HOH HOH . 
I 5 HOH A 40 1040 5 HOH HOH . 
I 5 HOH A 41 1041 40 HOH HOH . 
I 5 HOH A 42 1042 63 HOH HOH . 
I 5 HOH A 43 1043 87 HOH HOH . 
J 5 HOH B 1 401 8 HOH HOH . 
J 5 HOH B 2 402 12 HOH HOH . 
J 5 HOH B 3 403 2 HOH HOH . 
J 5 HOH B 4 404 114 HOH HOH . 
J 5 HOH B 5 405 13 HOH HOH . 
J 5 HOH B 6 406 1 HOH HOH . 
J 5 HOH B 7 407 3 HOH HOH . 
J 5 HOH B 8 408 10 HOH HOH . 
J 5 HOH B 9 409 11 HOH HOH . 
J 5 HOH B 10 410 15 HOH HOH . 
J 5 HOH B 11 411 109 HOH HOH . 
J 5 HOH B 12 412 113 HOH HOH . 
J 5 HOH B 13 413 117 HOH HOH . 
K 5 HOH C 1 401 105 HOH HOH . 
K 5 HOH C 2 402 18 HOH HOH . 
K 5 HOH C 3 403 56 HOH HOH . 
K 5 HOH C 4 404 29 HOH HOH . 
K 5 HOH C 5 405 31 HOH HOH . 
K 5 HOH C 6 406 9 HOH HOH . 
K 5 HOH C 7 407 103 HOH HOH . 
K 5 HOH C 8 408 19 HOH HOH . 
K 5 HOH C 9 409 17 HOH HOH . 
K 5 HOH C 10 410 26 HOH HOH . 
K 5 HOH C 11 411 28 HOH HOH . 
K 5 HOH C 12 412 27 HOH HOH . 
K 5 HOH C 13 413 24 HOH HOH . 
K 5 HOH C 14 414 16 HOH HOH . 
K 5 HOH C 15 415 104 HOH HOH . 
K 5 HOH C 16 416 25 HOH HOH . 
K 5 HOH C 17 417 30 HOH HOH . 
L 5 HOH D 1 1001 59 HOH HOH . 
L 5 HOH D 2 1002 20 HOH HOH . 
L 5 HOH D 3 1003 50 HOH HOH . 
L 5 HOH D 4 1004 52 HOH HOH . 
L 5 HOH D 5 1005 48 HOH HOH . 
L 5 HOH D 6 1006 49 HOH HOH . 
L 5 HOH D 7 1007 45 HOH HOH . 
L 5 HOH D 8 1008 98 HOH HOH . 
L 5 HOH D 9 1009 74 HOH HOH . 
L 5 HOH D 10 1010 61 HOH HOH . 
L 5 HOH D 11 1011 106 HOH HOH . 
L 5 HOH D 12 1012 57 HOH HOH . 
L 5 HOH D 13 1013 89 HOH HOH . 
L 5 HOH D 14 1014 116 HOH HOH . 
L 5 HOH D 15 1015 44 HOH HOH . 
L 5 HOH D 16 1016 55 HOH HOH . 
L 5 HOH D 17 1017 32 HOH HOH . 
L 5 HOH D 18 1018 23 HOH HOH . 
L 5 HOH D 19 1019 41 HOH HOH . 
L 5 HOH D 20 1020 36 HOH HOH . 
L 5 HOH D 21 1021 62 HOH HOH . 
L 5 HOH D 22 1022 51 HOH HOH . 
L 5 HOH D 23 1023 21 HOH HOH . 
L 5 HOH D 24 1024 53 HOH HOH . 
L 5 HOH D 25 1025 47 HOH HOH . 
L 5 HOH D 26 1026 108 HOH HOH . 
L 5 HOH D 27 1027 60 HOH HOH . 
L 5 HOH D 28 1028 33 HOH HOH . 
L 5 HOH D 29 1029 37 HOH HOH . 
L 5 HOH D 30 1030 107 HOH HOH . 
L 5 HOH D 31 1031 115 HOH HOH . 
L 5 HOH D 32 1032 54 HOH HOH . 
L 5 HOH D 33 1033 22 HOH HOH . 
L 5 HOH D 34 1034 72 HOH HOH . 
L 5 HOH D 35 1035 38 HOH HOH . 
L 5 HOH D 36 1036 42 HOH HOH . 
L 5 HOH D 37 1037 34 HOH HOH . 
L 5 HOH D 38 1038 58 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 4 -17.747 21.156 -24.346 1 29.7 ? N SAH 902 A 1 
HETATM 2 C CA SAH . . . F 4 -18.565 20.081 -24.898 1 38.59 ? CA SAH 902 A 1 
HETATM 3 C CB SAH . . . F 4 -18.28 19.899 -26.386 1 44.17 ? CB SAH 902 A 1 
HETATM 4 C CG SAH . . . F 4 -17.673 21.098 -27.109 1 37.05 ? CG SAH 902 A 1 
HETATM 5 S SD SAH . . . F 4 -17.305 20.695 -28.836 1 47.09 ? SD SAH 902 A 1 
HETATM 6 C C SAH . . . F 4 -18.359 18.755 -24.168 1 36.57 ? C SAH 902 A 1 
HETATM 7 O O SAH . . . F 4 -17.65 18.68 -23.162 1 42.73 ? O SAH 902 A 1 
HETATM 8 O OXT SAH . . . F 4 -18.909 17.726 -24.564 1 28.23 ? OXT SAH 902 A 1 
HETATM 9 C C5' SAH . . . F 4 -18.494 21.918 -29.447 1 44.23 ? C5' SAH 902 A 1 
HETATM 10 C C4' SAH . . . F 4 -19.922 21.39 -29.569 1 39.68 ? C4' SAH 902 A 1 
HETATM 11 O O4' SAH . . . F 4 -20.762 22.423 -30.047 1 42.91 ? O4' SAH 902 A 1 
HETATM 12 C C3' SAH . . . F 4 -20.054 20.232 -30.547 1 38.18 ? C3' SAH 902 A 1 
HETATM 13 O O3' SAH . . . F 4 -20.574 19.111 -29.871 1 44.69 ? O3' SAH 902 A 1 
HETATM 14 C C2' SAH . . . F 4 -21.054 20.687 -31.588 1 24.85 ? C2' SAH 902 A 1 
HETATM 15 O O2' SAH . . . F 4 -22.014 19.689 -31.832 1 29.89 ? O2' SAH 902 A 1 
HETATM 16 C C1' SAH . . . F 4 -21.711 21.896 -30.951 1 35.89 ? C1' SAH 902 A 1 
HETATM 17 N N9 SAH . . . F 4 -22.109 22.892 -31.959 1 35.15 ? N9 SAH 902 A 1 
HETATM 18 C C8 SAH . . . F 4 -21.501 23.137 -33.163 1 28.81 ? C8 SAH 902 A 1 
HETATM 19 N N7 SAH . . . F 4 -22.18 24.128 -33.786 1 36.29 ? N7 SAH 902 A 1 
HETATM 20 C C5 SAH . . . F 4 -23.209 24.515 -33.001 1 34.07 ? C5 SAH 902 A 1 
HETATM 21 C C6 SAH . . . F 4 -24.199 25.477 -33.156 1 39.74 ? C6 SAH 902 A 1 
HETATM 22 N N6 SAH . . . F 4 -24.239 26.222 -34.258 1 33.88 ? N6 SAH 902 A 1 
HETATM 23 N N1 SAH . . . F 4 -25.141 25.655 -32.162 1 42.65 ? N1 SAH 902 A 1 
HETATM 24 C C2 SAH . . . F 4 -25.091 24.877 -31.022 1 30.75 ? C2 SAH 902 A 1 
HETATM 25 N N3 SAH . . . F 4 -24.104 23.923 -30.873 1 26.74 ? N3 SAH 902 A 1 
HETATM 26 C C4 SAH . . . F 4 -23.178 23.745 -31.848 1 37.57 ? C4 SAH 902 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           258 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#