data_3LHD
#
_model_server_result.job_id            xTtXOZAhsB6Q2RQTGQjSuw 
_model_server_result.datetime_utc      '2024-11-23 07:24:59' 
_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          3lhd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":301}' 
#
_entry.id    3LHD 
#
_exptl.entry_id    3LHD 
_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    4 
_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            3LHD 
_cell.length_a            66.03 
_cell.length_b            127.577 
_cell.length_c            151.396 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3LHD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,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
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H 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
disulf ? disulf1 A SG CYS 196 C CYS 196 1_555 B SG CYS 233 A CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf2 A SG CYS 233 C CYS 233 1_555 B SG CYS 196 A CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf3 C SG CYS 196 B CYS 196 1_555 D SG CYS 233 D CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
disulf ? disulf4 C SG CYS 233 B CYS 233 1_555 D SG CYS 196 D CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
#
_chem_comp.formula           'C14 H20 N6 O5 S' 
_chem_comp.formula_weight    384.411 
_chem_comp.id                SAH 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              S-ADENOSYL-L-HOMOCYSTEINE 
_chem_comp.type              non-polymer 
_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                     3LHD 
_atom_sites.fract_transf_matrix[1][1]    0.015145 
_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]    0.007838 
_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]    0.006605 
_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 2 SAH C 1 301 301 SAH SAH . 
F 2 SAH A 1 301 301 SAH SAH . 
G 2 SAH B 1 301 301 SAH SAH . 
H 2 SAH D 1 301 301 SAH SAH . 
I 3 HOH C 1 254 1 HOH HOH . 
I 3 HOH C 2 255 7 HOH HOH . 
I 3 HOH C 3 256 8 HOH HOH . 
I 3 HOH C 4 257 15 HOH HOH . 
I 3 HOH C 5 258 16 HOH HOH . 
I 3 HOH C 6 259 22 HOH HOH . 
I 3 HOH C 7 260 25 HOH HOH . 
I 3 HOH C 8 261 28 HOH HOH . 
I 3 HOH C 9 262 30 HOH HOH . 
I 3 HOH C 10 263 32 HOH HOH . 
I 3 HOH C 11 264 33 HOH HOH . 
I 3 HOH C 12 265 34 HOH HOH . 
I 3 HOH C 13 266 36 HOH HOH . 
I 3 HOH C 14 267 42 HOH HOH . 
I 3 HOH C 15 268 44 HOH HOH . 
I 3 HOH C 16 269 50 HOH HOH . 
I 3 HOH C 17 270 58 HOH HOH . 
I 3 HOH C 18 271 60 HOH HOH . 
I 3 HOH C 19 272 62 HOH HOH . 
I 3 HOH C 20 273 64 HOH HOH . 
I 3 HOH C 21 274 65 HOH HOH . 
I 3 HOH C 22 275 67 HOH HOH . 
I 3 HOH C 23 276 77 HOH HOH . 
I 3 HOH C 24 277 81 HOH HOH . 
I 3 HOH C 25 278 84 HOH HOH . 
I 3 HOH C 26 279 86 HOH HOH . 
I 3 HOH C 27 280 87 HOH HOH . 
I 3 HOH C 28 281 88 HOH HOH . 
I 3 HOH C 29 282 92 HOH HOH . 
I 3 HOH C 30 283 104 HOH HOH . 
I 3 HOH C 31 284 107 HOH HOH . 
I 3 HOH C 32 285 109 HOH HOH . 
I 3 HOH C 33 286 117 HOH HOH . 
I 3 HOH C 34 287 120 HOH HOH . 
I 3 HOH C 35 288 127 HOH HOH . 
I 3 HOH C 36 289 131 HOH HOH . 
I 3 HOH C 37 290 135 HOH HOH . 
I 3 HOH C 38 291 141 HOH HOH . 
I 3 HOH C 39 292 142 HOH HOH . 
J 3 HOH A 1 254 5 HOH HOH . 
J 3 HOH A 2 255 6 HOH HOH . 
J 3 HOH A 3 256 17 HOH HOH . 
J 3 HOH A 4 257 21 HOH HOH . 
J 3 HOH A 5 258 27 HOH HOH . 
J 3 HOH A 6 259 29 HOH HOH . 
J 3 HOH A 7 260 31 HOH HOH . 
J 3 HOH A 8 261 35 HOH HOH . 
J 3 HOH A 9 262 39 HOH HOH . 
J 3 HOH A 10 263 49 HOH HOH . 
J 3 HOH A 11 264 61 HOH HOH . 
J 3 HOH A 12 265 70 HOH HOH . 
J 3 HOH A 13 266 71 HOH HOH . 
J 3 HOH A 14 267 83 HOH HOH . 
J 3 HOH A 15 268 95 HOH HOH . 
J 3 HOH A 16 269 99 HOH HOH . 
J 3 HOH A 17 270 101 HOH HOH . 
J 3 HOH A 18 271 115 HOH HOH . 
J 3 HOH A 19 272 121 HOH HOH . 
J 3 HOH A 20 273 130 HOH HOH . 
J 3 HOH A 21 274 134 HOH HOH . 
J 3 HOH A 22 275 136 HOH HOH . 
J 3 HOH A 23 276 138 HOH HOH . 
K 3 HOH B 1 254 11 HOH HOH . 
K 3 HOH B 2 255 19 HOH HOH . 
K 3 HOH B 3 256 23 HOH HOH . 
K 3 HOH B 4 257 37 HOH HOH . 
K 3 HOH B 5 258 38 HOH HOH . 
K 3 HOH B 6 259 40 HOH HOH . 
K 3 HOH B 7 260 47 HOH HOH . 
K 3 HOH B 8 261 53 HOH HOH . 
K 3 HOH B 9 262 57 HOH HOH . 
K 3 HOH B 10 263 63 HOH HOH . 
K 3 HOH B 11 264 68 HOH HOH . 
K 3 HOH B 12 265 75 HOH HOH . 
K 3 HOH B 13 266 80 HOH HOH . 
K 3 HOH B 14 267 82 HOH HOH . 
K 3 HOH B 15 268 85 HOH HOH . 
K 3 HOH B 16 269 93 HOH HOH . 
K 3 HOH B 17 270 100 HOH HOH . 
K 3 HOH B 18 271 103 HOH HOH . 
K 3 HOH B 19 272 113 HOH HOH . 
K 3 HOH B 20 273 114 HOH HOH . 
K 3 HOH B 21 274 118 HOH HOH . 
K 3 HOH B 22 275 119 HOH HOH . 
K 3 HOH B 23 276 122 HOH HOH . 
K 3 HOH B 24 277 125 HOH HOH . 
K 3 HOH B 25 278 126 HOH HOH . 
K 3 HOH B 26 279 128 HOH HOH . 
K 3 HOH B 27 280 133 HOH HOH . 
K 3 HOH B 28 281 139 HOH HOH . 
K 3 HOH B 29 282 140 HOH HOH . 
L 3 HOH D 1 254 2 HOH HOH . 
L 3 HOH D 2 255 4 HOH HOH . 
L 3 HOH D 3 256 10 HOH HOH . 
L 3 HOH D 4 257 12 HOH HOH . 
L 3 HOH D 5 258 13 HOH HOH . 
L 3 HOH D 6 259 14 HOH HOH . 
L 3 HOH D 7 260 18 HOH HOH . 
L 3 HOH D 8 261 20 HOH HOH . 
L 3 HOH D 9 262 26 HOH HOH . 
L 3 HOH D 10 263 41 HOH HOH . 
L 3 HOH D 11 264 43 HOH HOH . 
L 3 HOH D 12 265 45 HOH HOH . 
L 3 HOH D 13 266 48 HOH HOH . 
L 3 HOH D 14 267 52 HOH HOH . 
L 3 HOH D 15 268 54 HOH HOH . 
L 3 HOH D 16 269 56 HOH HOH . 
L 3 HOH D 17 270 59 HOH HOH . 
L 3 HOH D 18 271 69 HOH HOH . 
L 3 HOH D 19 272 72 HOH HOH . 
L 3 HOH D 20 273 73 HOH HOH . 
L 3 HOH D 21 274 74 HOH HOH . 
L 3 HOH D 22 275 78 HOH HOH . 
L 3 HOH D 23 276 89 HOH HOH . 
L 3 HOH D 24 277 90 HOH HOH . 
L 3 HOH D 25 278 91 HOH HOH . 
L 3 HOH D 26 279 96 HOH HOH . 
L 3 HOH D 27 280 97 HOH HOH . 
L 3 HOH D 28 281 98 HOH HOH . 
L 3 HOH D 29 282 102 HOH HOH . 
L 3 HOH D 30 283 105 HOH HOH . 
L 3 HOH D 31 284 106 HOH HOH . 
L 3 HOH D 32 285 108 HOH HOH . 
L 3 HOH D 33 286 111 HOH HOH . 
L 3 HOH D 34 287 112 HOH HOH . 
L 3 HOH D 35 288 116 HOH HOH . 
L 3 HOH D 36 289 123 HOH HOH . 
L 3 HOH D 37 290 124 HOH HOH . 
L 3 HOH D 38 291 129 HOH HOH . 
L 3 HOH D 39 292 132 HOH HOH . 
L 3 HOH D 40 293 137 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 . . . E 2 -6.066 -24.857 -32.927 1 64.11 ? N SAH 301 C 1 
HETATM 2 C CA SAH . . . E 2 -7.447 -25.126 -33.45 1 63.97 ? CA SAH 301 C 1 
HETATM 3 C CB SAH . . . E 2 -8.423 -25.279 -32.274 1 63.63 ? CB SAH 301 C 1 
HETATM 4 C CG SAH . . . E 2 -8.789 -26.735 -31.982 1 61.77 ? CG SAH 301 C 1 
HETATM 5 S SD SAH . . . E 2 -10.271 -26.816 -31.011 1 58.56 ? SD SAH 301 C 1 
HETATM 6 C C SAH . . . E 2 -7.851 -24 -34.38 1 64.3 ? C SAH 301 C 1 
HETATM 7 O O SAH . . . E 2 -7.086 -23.609 -35.27 1 64.4 ? O SAH 301 C 1 
HETATM 8 O OXT SAH . . . E 2 -8.945 -23.428 -34.293 1 64.51 ? OXT SAH 301 C 1 
HETATM 9 C C5' SAH . . . E 2 -9.62 -26.981 -29.37 1 53.49 ? C5' SAH 301 C 1 
HETATM 10 C C4' SAH . . . E 2 -10.465 -27.882 -28.459 1 50.01 ? C4' SAH 301 C 1 
HETATM 11 O O4' SAH . . . E 2 -11.732 -27.292 -28.127 1 48.22 ? O4' SAH 301 C 1 
HETATM 12 C C3' SAH . . . E 2 -10.794 -29.233 -29.064 1 48.68 ? C3' SAH 301 C 1 
HETATM 13 O O3' SAH . . . E 2 -10.563 -30.19 -28.033 1 48.24 ? O3' SAH 301 C 1 
HETATM 14 C C2' SAH . . . E 2 -12.27 -29.147 -29.41 1 47.11 ? C2' SAH 301 C 1 
HETATM 15 O O2' SAH . . . E 2 -12.912 -30.422 -29.423 1 47.32 ? O2' SAH 301 C 1 
HETATM 16 C C1' SAH . . . E 2 -12.788 -28.234 -28.314 1 46.21 ? C1' SAH 301 C 1 
HETATM 17 N N9 SAH . . . E 2 -14.012 -27.478 -28.641 1 44.29 ? N9 SAH 301 C 1 
HETATM 18 C C8 SAH . . . E 2 -14.331 -26.918 -29.821 1 43.39 ? C8 SAH 301 C 1 
HETATM 19 N N7 SAH . . . E 2 -15.527 -26.278 -29.744 1 43.39 ? N7 SAH 301 C 1 
HETATM 20 C C5 SAH . . . E 2 -15.988 -26.426 -28.492 1 43.39 ? C5 SAH 301 C 1 
HETATM 21 C C6 SAH . . . E 2 -17.186 -26.006 -27.735 1 43.94 ? C6 SAH 301 C 1 
HETATM 22 N N6 SAH . . . E 2 -18.154 -25.282 -28.337 1 44.61 ? N6 SAH 301 C 1 
HETATM 23 N N1 SAH . . . E 2 -17.289 -26.363 -26.431 1 43.91 ? N1 SAH 301 C 1 
HETATM 24 C C2 SAH . . . E 2 -16.329 -27.089 -25.831 1 43.91 ? C2 SAH 301 C 1 
HETATM 25 N N3 SAH . . . E 2 -15.215 -27.505 -26.463 1 44.49 ? N3 SAH 301 C 1 
HETATM 26 C C4 SAH . . . E 2 -14.985 -27.212 -27.768 1 44.12 ? C4 SAH 301 C 1 
#
_model_server_stats.io_time_ms              68 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           26 
#