data_5GP1
#
_model_server_result.job_id            JYyuPMUhgPvtgE7UbuYa8g 
_model_server_result.datetime_utc      '2024-11-08 03:08:31' 
_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          5gp1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":307}' 
#
_entry.id    5GP1 
#
_exptl.entry_id    5GP1 
_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    3 
_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         120 
_cell.entry_id            5GP1 
_cell.length_a            123.77 
_cell.length_b            123.77 
_cell.length_c            119.36 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GP1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61' 
#
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 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,H,I,J,S 1 1 
B,K,L,M,N,T 2 1 
C,O,P,Q,R,U 3 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 J N N 
? 4 N N N 
? 4 R 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
covale ? covale1 A NZ LYS 30 A LYS 29 1_555 D O3 SO4 . A SO4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? 
covale ? covale2 A NE ARG 42 A ARG 41 1_555 E O3 SO4 . A SO4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? 
#
_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     ? 
#
_atom_sites.entry_id                     5GP1 
_atom_sites.fract_transf_matrix[1][1]    0.00808 
_atom_sites.fract_transf_matrix[1][2]    0.004665 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009329 
_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]    0.008378 
_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
D 2 SO4 A 1 301 267 SO4 SO4 . 
E 2 SO4 A 1 302 268 SO4 SO4 . 
F 2 SO4 A 1 303 269 SO4 SO4 . 
G 2 SO4 A 1 304 270 SO4 SO4 . 
H 2 SO4 A 1 305 297 SO4 SO4 . 
I 3 GTA A 1 306 266 GTA GTA . 
J 4 SAH A 1 307 298 SAH SAH . 
K 2 SO4 B 1 301 267 SO4 SO4 . 
L 2 SO4 B 1 302 285 SO4 SO4 . 
M 3 GTA B 1 303 266 GTA GTA . 
N 4 SAH B 1 304 286 SAH SAH . 
O 2 SO4 C 1 301 266 SO4 SO4 . 
P 5 NI C 1 302 288 NI NI . 
Q 3 GTA C 1 303 265 GTA GTA . 
R 4 SAH C 1 304 289 SAH SAH . 
S 6 HOH A 1 401 286 HOH HOH . 
S 6 HOH A 2 402 287 HOH HOH . 
S 6 HOH A 3 403 282 HOH HOH . 
S 6 HOH A 4 404 281 HOH HOH . 
S 6 HOH A 5 405 302 HOH HOH . 
S 6 HOH A 6 406 283 HOH HOH . 
S 6 HOH A 7 407 272 HOH HOH . 
S 6 HOH A 8 408 292 HOH HOH . 
S 6 HOH A 9 409 277 HOH HOH . 
S 6 HOH A 10 410 278 HOH HOH . 
S 6 HOH A 11 411 274 HOH HOH . 
S 6 HOH A 12 412 285 HOH HOH . 
S 6 HOH A 13 413 299 HOH HOH . 
S 6 HOH A 14 414 279 HOH HOH . 
S 6 HOH A 15 415 291 HOH HOH . 
S 6 HOH A 16 416 294 HOH HOH . 
S 6 HOH A 17 417 289 HOH HOH . 
S 6 HOH A 18 418 295 HOH HOH . 
S 6 HOH A 19 419 290 HOH HOH . 
S 6 HOH A 20 420 284 HOH HOH . 
S 6 HOH A 21 421 288 HOH HOH . 
S 6 HOH A 22 422 276 HOH HOH . 
S 6 HOH A 23 423 293 HOH HOH . 
S 6 HOH A 24 424 296 HOH HOH . 
S 6 HOH A 25 425 280 HOH HOH . 
S 6 HOH A 26 426 300 HOH HOH . 
S 6 HOH A 27 427 273 HOH HOH . 
S 6 HOH A 28 428 271 HOH HOH . 
S 6 HOH A 29 429 303 HOH HOH . 
S 6 HOH A 30 430 301 HOH HOH . 
S 6 HOH A 31 431 275 HOH HOH . 
T 6 HOH B 1 401 275 HOH HOH . 
T 6 HOH B 2 402 278 HOH HOH . 
T 6 HOH B 3 403 270 HOH HOH . 
T 6 HOH B 4 404 287 HOH HOH . 
T 6 HOH B 5 405 284 HOH HOH . 
T 6 HOH B 6 406 277 HOH HOH . 
T 6 HOH B 7 407 272 HOH HOH . 
T 6 HOH B 8 408 279 HOH HOH . 
T 6 HOH B 9 409 268 HOH HOH . 
T 6 HOH B 10 410 273 HOH HOH . 
T 6 HOH B 11 411 287 HOH HOH . 
T 6 HOH B 12 412 276 HOH HOH . 
T 6 HOH B 13 413 280 HOH HOH . 
T 6 HOH B 14 414 281 HOH HOH . 
T 6 HOH B 15 415 271 HOH HOH . 
T 6 HOH B 16 416 282 HOH HOH . 
T 6 HOH B 17 417 283 HOH HOH . 
T 6 HOH B 18 418 274 HOH HOH . 
T 6 HOH B 19 419 288 HOH HOH . 
U 6 HOH C 1 401 269 HOH HOH . 
U 6 HOH C 2 402 271 HOH HOH . 
U 6 HOH C 3 403 282 HOH HOH . 
U 6 HOH C 4 404 270 HOH HOH . 
U 6 HOH C 5 405 284 HOH HOH . 
U 6 HOH C 6 406 279 HOH HOH . 
U 6 HOH C 7 407 290 HOH HOH . 
U 6 HOH C 8 408 276 HOH HOH . 
U 6 HOH C 9 409 268 HOH HOH . 
U 6 HOH C 10 410 267 HOH HOH . 
U 6 HOH C 11 411 278 HOH HOH . 
U 6 HOH C 12 412 286 HOH HOH . 
U 6 HOH C 13 413 280 HOH HOH . 
U 6 HOH C 14 414 285 HOH HOH . 
U 6 HOH C 15 415 274 HOH HOH . 
U 6 HOH C 16 416 277 HOH HOH . 
U 6 HOH C 17 417 291 HOH HOH . 
U 6 HOH C 18 418 281 HOH HOH . 
U 6 HOH C 19 419 272 HOH HOH . 
U 6 HOH C 20 420 283 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 . . . J 4 33.46 124.842 -11.288 1 35.77 ? N SAH 307 A 1 
HETATM 2 C CA SAH . . . J 4 32.801 126.084 -10.903 1 36.21 ? CA SAH 307 A 1 
HETATM 3 C CB SAH . . . J 4 32.224 125.968 -9.496 1 47.4 ? CB SAH 307 A 1 
HETATM 4 C CG SAH . . . J 4 33.099 125.217 -8.499 1 48.81 ? CG SAH 307 A 1 
HETATM 5 S SD SAH . . . J 4 32.527 125.442 -6.795 1 50.01 ? SD SAH 307 A 1 
HETATM 6 C C SAH . . . J 4 33.757 127.267 -10.983 1 31.68 ? C SAH 307 A 1 
HETATM 7 O O SAH . . . J 4 34.969 127.09 -11.088 1 33.19 -1 O SAH 307 A 1 
HETATM 8 O OXT SAH . . . J 4 33.339 128.424 -10.944 1 30.35 ? OXT SAH 307 A 1 
HETATM 9 C C5' SAH . . . J 4 32.312 123.654 -6.6 1 46.98 ? C5' SAH 307 A 1 
HETATM 10 C C4' SAH . . . J 4 30.852 123.23 -6.712 1 43.9 ? C4' SAH 307 A 1 
HETATM 11 O O4' SAH . . . J 4 30.74 121.822 -6.692 1 39.06 ? O4' SAH 307 A 1 
HETATM 12 C C3' SAH . . . J 4 30.004 123.744 -5.557 1 45.91 ? C3' SAH 307 A 1 
HETATM 13 O O3' SAH . . . J 4 29.191 124.814 -5.98 1 48.05 ? O3' SAH 307 A 1 
HETATM 14 C C2' SAH . . . J 4 29.144 122.569 -5.137 1 40.34 ? C2' SAH 307 A 1 
HETATM 15 O O2' SAH . . . J 4 27.779 122.885 -5.272 1 44.5 ? O2' SAH 307 A 1 
HETATM 16 C C1' SAH . . . J 4 29.499 121.471 -6.117 1 38.25 ? C1' SAH 307 A 1 
HETATM 17 N N9 SAH . . . J 4 29.559 120.156 -5.458 1 45.74 ? N9 SAH 307 A 1 
HETATM 18 C C8 SAH . . . J 4 30.303 119.809 -4.362 1 47.87 ? C8 SAH 307 A 1 
HETATM 19 N N7 SAH . . . J 4 30.068 118.504 -4.086 1 49.78 ? N7 SAH 307 A 1 
HETATM 20 C C5 SAH . . . J 4 29.186 118.019 -4.989 1 50.18 ? C5 SAH 307 A 1 
HETATM 21 C C6 SAH . . . J 4 28.609 116.767 -5.167 1 43.51 ? C6 SAH 307 A 1 
HETATM 22 N N6 SAH . . . J 4 28.91 115.768 -4.346 1 43.95 ? N6 SAH 307 A 1 
HETATM 23 N N1 SAH . . . J 4 27.721 116.565 -6.202 1 40.53 ? N1 SAH 307 A 1 
HETATM 24 C C2 SAH . . . J 4 27.408 117.605 -7.052 1 45.07 ? C2 SAH 307 A 1 
HETATM 25 N N3 SAH . . . J 4 27.985 118.845 -6.873 1 50.28 ? N3 SAH 307 A 1 
HETATM 26 C C4 SAH . . . J 4 28.859 119.049 -5.858 1 52.33 ? C4 SAH 307 A 1 
#
_model_server_stats.io_time_ms              31 
_model_server_stats.parse_time_ms           30 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           242 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           26 
#