data_8SWR
#
_model_server_result.job_id            FaKtX9aUnt2aZMNarhnDCw 
_model_server_result.datetime_utc      '2024-11-05 19:39:28' 
_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          8swr 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":400}' 
#
_entry.id    8SWR 
#
_exptl.entry_id    8SWR 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              279.295 
_entity.id                          2 
_entity.src_method                  nat 
_entity.type                        non-polymer 
_entity.pdbx_description            2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one 
_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          108.3 
_cell.angle_gamma         90 
_cell.entry_id            8SWR 
_cell.length_a            89.43 
_cell.length_b            111.005 
_cell.length_c            97.87 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8SWR 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 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,B,C,G,H,I,M,N,O 1 1 
D,E,F,J,K,L,P,Q,R 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
? 2 G N N 
? 2 I N N 
? 2 J N N 
#
_chem_comp.formula           'C12 H17 N5 O3' 
_chem_comp.formula_weight    279.295 
_chem_comp.id                IM5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-amino-7-{[(3R,4R)-3-hydroxy-4-(hydroxymethyl)pyrrolidin-1-yl]methyl}-3,5-dihydro-4H-pyrrolo[3,2-d]pyrimidin-4-one 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     DADMe-ImmG 
#
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
C2 N1 IM5 sing 190 n n 
N1 C6 IM5 sing 191 n n 
N1 HN1 IM5 sing 192 n n 
N2 C2 IM5 sing 193 n n 
N3 C2 IM5 doub 194 n n 
N2 HN2 IM5 sing 195 n n 
N2 HN2A IM5 sing 196 n n 
N3 C4 IM5 sing 197 n n 
C9 C4 IM5 sing 198 n y 
C4 C5 IM5 doub 199 n y 
C5 N7 IM5 sing 200 n y 
C5 C6 IM5 sing 201 n n 
C6 O6 IM5 doub 202 n n 
C8 N7 IM5 sing 203 n y 
C9 C8 IM5 doub 204 n y 
C8 H8 IM5 sing 205 n n 
C10 C9 IM5 sing 206 n n 
C10 N1' IM5 sing 207 n n 
N1' C2' IM5 sing 208 n n 
N1' C6' IM5 sing 209 n n 
C10 H10 IM5 sing 210 n n 
C10 H10A IM5 sing 211 n n 
C2' C3' IM5 sing 212 n n 
C2' H2' IM5 sing 213 n n 
C2' "H2'A" IM5 sing 214 n n 
O3' C3' IM5 sing 215 n n 
C3' C4' IM5 sing 216 n n 
C3' H3' IM5 sing 217 n n 
O3' HO3' IM5 sing 218 n n 
C6' C4' IM5 sing 219 n n 
C4' C5' IM5 sing 220 n n 
C4' H4' IM5 sing 221 n n 
C5' O5' IM5 sing 222 n n 
C5' H5' IM5 sing 223 n n 
C5' "H5'A" IM5 sing 224 n n 
O5' HO5' IM5 sing 225 n n 
C6' H6' IM5 sing 226 n n 
C6' "H6'A" IM5 sing 227 n n 
N7 HN7 IM5 sing 228 n n 
#
_atom_sites.entry_id                     8SWR 
_atom_sites.fract_transf_matrix[1][1]    0.011182 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003698 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009009 
_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]    0.010762 
_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
G 2 IM5 A 1 400 400 IM5 IM5 . 
H 3 SO4 A 1 401 401 SO4 SO4 . 
I 2 IM5 B 1 400 400 IM5 IM5 . 
J 2 IM5 D 1 400 400 IM5 IM5 . 
K 3 SO4 D 1 401 401 SO4 SO4 . 
L 4 GUN E 1 400 400 GUN GUN . 
M 5 HOH A 1 501 12 HOH HOH . 
M 5 HOH A 2 502 40 HOH HOH . 
M 5 HOH A 3 503 45 HOH HOH . 
M 5 HOH A 4 504 11 HOH HOH . 
M 5 HOH A 5 505 97 HOH HOH . 
M 5 HOH A 6 506 3 HOH HOH . 
M 5 HOH A 7 507 15 HOH HOH . 
M 5 HOH A 8 508 23 HOH HOH . 
M 5 HOH A 9 509 96 HOH HOH . 
M 5 HOH A 10 510 10 HOH HOH . 
M 5 HOH A 11 511 99 HOH HOH . 
M 5 HOH A 12 512 54 HOH HOH . 
M 5 HOH A 13 513 25 HOH HOH . 
M 5 HOH A 14 514 29 HOH HOH . 
M 5 HOH A 15 515 95 HOH HOH . 
M 5 HOH A 16 516 34 HOH HOH . 
M 5 HOH A 17 517 39 HOH HOH . 
M 5 HOH A 18 518 87 HOH HOH . 
M 5 HOH A 19 519 75 HOH HOH . 
M 5 HOH A 20 520 35 HOH HOH . 
M 5 HOH A 21 521 60 HOH HOH . 
M 5 HOH A 22 522 80 HOH HOH . 
M 5 HOH A 23 523 98 HOH HOH . 
N 5 HOH B 1 501 66 HOH HOH . 
N 5 HOH B 2 502 38 HOH HOH . 
N 5 HOH B 3 503 79 HOH HOH . 
N 5 HOH B 4 504 14 HOH HOH . 
N 5 HOH B 5 505 42 HOH HOH . 
N 5 HOH B 6 506 69 HOH HOH . 
N 5 HOH B 7 507 86 HOH HOH . 
N 5 HOH B 8 508 85 HOH HOH . 
N 5 HOH B 9 509 61 HOH HOH . 
N 5 HOH B 10 510 63 HOH HOH . 
N 5 HOH B 11 511 9 HOH HOH . 
N 5 HOH B 12 512 76 HOH HOH . 
N 5 HOH B 13 513 74 HOH HOH . 
N 5 HOH B 14 514 50 HOH HOH . 
N 5 HOH B 15 515 88 HOH HOH . 
O 5 HOH C 1 401 81 HOH HOH . 
O 5 HOH C 2 402 46 HOH HOH . 
O 5 HOH C 3 403 78 HOH HOH . 
O 5 HOH C 4 404 82 HOH HOH . 
O 5 HOH C 5 405 53 HOH HOH . 
O 5 HOH C 6 406 28 HOH HOH . 
O 5 HOH C 7 407 36 HOH HOH . 
P 5 HOH D 1 501 51 HOH HOH . 
P 5 HOH D 2 502 33 HOH HOH . 
P 5 HOH D 3 503 65 HOH HOH . 
P 5 HOH D 4 504 2 HOH HOH . 
P 5 HOH D 5 505 91 HOH HOH . 
P 5 HOH D 6 506 19 HOH HOH . 
P 5 HOH D 7 507 32 HOH HOH . 
P 5 HOH D 8 508 13 HOH HOH . 
P 5 HOH D 9 509 30 HOH HOH . 
P 5 HOH D 10 510 83 HOH HOH . 
P 5 HOH D 11 511 20 HOH HOH . 
P 5 HOH D 12 512 21 HOH HOH . 
P 5 HOH D 13 513 64 HOH HOH . 
P 5 HOH D 14 514 100 HOH HOH . 
P 5 HOH D 15 515 59 HOH HOH . 
P 5 HOH D 16 516 26 HOH HOH . 
P 5 HOH D 17 517 101 HOH HOH . 
P 5 HOH D 18 518 90 HOH HOH . 
P 5 HOH D 19 519 93 HOH HOH . 
P 5 HOH D 20 520 92 HOH HOH . 
P 5 HOH D 21 521 77 HOH HOH . 
Q 5 HOH E 1 501 24 HOH HOH . 
Q 5 HOH E 2 502 47 HOH HOH . 
Q 5 HOH E 3 503 72 HOH HOH . 
Q 5 HOH E 4 504 67 HOH HOH . 
Q 5 HOH E 5 505 89 HOH HOH . 
Q 5 HOH E 6 506 73 HOH HOH . 
Q 5 HOH E 7 507 68 HOH HOH . 
Q 5 HOH E 8 508 31 HOH HOH . 
Q 5 HOH E 9 509 27 HOH HOH . 
R 5 HOH F 1 401 84 HOH HOH . 
R 5 HOH F 2 402 17 HOH HOH . 
R 5 HOH F 3 403 1 HOH HOH . 
R 5 HOH F 4 404 22 HOH HOH . 
R 5 HOH F 5 405 70 HOH HOH . 
R 5 HOH F 6 406 71 HOH HOH . 
R 5 HOH F 7 407 52 HOH HOH . 
R 5 HOH F 8 408 37 HOH HOH . 
R 5 HOH F 9 409 18 HOH HOH . 
R 5 HOH F 10 410 7 HOH HOH . 
R 5 HOH F 11 411 6 HOH HOH . 
R 5 HOH F 12 412 44 HOH HOH . 
R 5 HOH F 13 413 62 HOH HOH . 
R 5 HOH F 14 414 16 HOH HOH . 
R 5 HOH F 15 415 41 HOH HOH . 
R 5 HOH F 16 416 43 HOH HOH . 
R 5 HOH F 17 417 4 HOH HOH . 
R 5 HOH F 18 418 57 HOH HOH . 
R 5 HOH F 19 419 5 HOH HOH . 
R 5 HOH F 20 420 8 HOH HOH . 
R 5 HOH F 21 421 49 HOH HOH . 
R 5 HOH F 22 422 56 HOH HOH . 
R 5 HOH F 23 423 48 HOH HOH . 
R 5 HOH F 24 424 55 HOH HOH . 
R 5 HOH F 25 425 94 HOH HOH . 
R 5 HOH F 26 426 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 N1 IM5 . . . I 2 91.121 10.813 176.999 1 38.66 ? N1 IM5 400 B 1 
HETATM 2 C C2 IM5 . . . I 2 92.111 10.722 177.945 1 44 ? C2 IM5 400 B 1 
HETATM 3 N N2 IM5 . . . I 2 91.829 11.182 179.172 1 42.05 ? N2 IM5 400 B 1 
HETATM 4 N N3 IM5 . . . I 2 93.298 10.206 177.679 1 41.92 ? N3 IM5 400 B 1 
HETATM 5 C C4 IM5 . . . I 2 93.513 9.754 176.408 1 43.21 ? C4 IM5 400 B 1 
HETATM 6 C C5 IM5 . . . I 2 92.534 9.83 175.408 1 46.95 ? C5 IM5 400 B 1 
HETATM 7 C C6 IM5 . . . I 2 91.25 10.384 175.683 1 44.44 ? C6 IM5 400 B 1 
HETATM 8 O O6 IM5 . . . I 2 90.307 10.503 174.89 1 39.47 ? O6 IM5 400 B 1 
HETATM 9 N N7 IM5 . . . I 2 93.083 9.297 174.268 1 44.71 ? N7 IM5 400 B 1 
HETATM 10 C C8 IM5 . . . I 2 94.364 8.907 174.541 1 45.71 ? C8 IM5 400 B 1 
HETATM 11 C C9 IM5 . . . I 2 94.644 9.169 175.852 1 45.03 ? C9 IM5 400 B 1 
HETATM 12 N N1' IM5 . . . I 2 96.199 7.553 177.055 1 56.84 ? N1' IM5 400 B 1 
HETATM 13 C C10 IM5 . . . I 2 95.935 8.913 176.569 1 54.15 ? C10 IM5 400 B 1 
HETATM 14 C C2' IM5 . . . I 2 95.675 7.202 178.377 0.66 52.44 ? C2' IM5 400 B 1 
HETATM 15 C C3' IM5 . . . I 2 96.072 5.745 178.471 0.44 57.13 ? C3' IM5 400 B 1 
HETATM 16 O O3' IM5 . . . I 2 97.427 5.62 178.877 0.88 64.27 ? O3' IM5 400 B 1 
HETATM 17 C C4' IM5 . . . I 2 95.936 5.221 177.029 0.67 55.3 ? C4' IM5 400 B 1 
HETATM 18 C C5' IM5 . . . I 2 94.866 4.165 176.833 0.81 50.13 ? C5' IM5 400 B 1 
HETATM 19 O O5' IM5 . . . I 2 93.567 4.685 177.069 0.71 47.53 ? O5' IM5 400 B 1 
HETATM 20 C C6' IM5 . . . I 2 95.637 6.486 176.227 0.37 55.46 ? C6' IM5 400 B 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    30 
_model_server_stats.query_time_ms           215 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           20 
#