data_3PHB
#
_model_server_result.job_id            ZxLVI3CS9JHM5Hv8ygUt7A 
_model_server_result.datetime_utc      '2024-11-25 15:29:02' 
_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          3phb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":290}' 
#
_entry.id    3PHB 
#
_exptl.entry_id    3PHB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              279.295 
_entity.id                          2 
_entity.src_method                  syn 
_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    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.33 
_cell.angle_gamma         90 
_cell.entry_id            3PHB 
_cell.length_a            269.27 
_cell.length_b            52.632 
_cell.length_c            128.119 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3PHB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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,F,G,H,I,J,K,L,U,V,W,X,Y,Z,DA 1 1 
C,D,E,M,N,O,P,Q,R,S,T,AA,BA,CA 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 J N N 
? 2 N N N 
? 2 Q N N 
? 2 S N N 
? 2 W 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 173 n n 
N1 C6 IM5 sing 174 n n 
N1 HN1 IM5 sing 175 n n 
N2 C2 IM5 sing 176 n n 
N3 C2 IM5 doub 177 n n 
N2 HN2 IM5 sing 178 n n 
N2 HN2A IM5 sing 179 n n 
N3 C4 IM5 sing 180 n n 
C9 C4 IM5 sing 181 n y 
C4 C5 IM5 doub 182 n y 
C5 N7 IM5 sing 183 n y 
C5 C6 IM5 sing 184 n n 
C6 O6 IM5 doub 185 n n 
C8 N7 IM5 sing 186 n y 
C9 C8 IM5 doub 187 n y 
C8 H8 IM5 sing 188 n n 
C10 C9 IM5 sing 189 n n 
C10 N1' IM5 sing 190 n n 
N1' C2' IM5 sing 191 n n 
N1' C6' IM5 sing 192 n n 
C10 H10 IM5 sing 193 n n 
C10 H10A IM5 sing 194 n n 
C2' C3' IM5 sing 195 n n 
C2' H2' IM5 sing 196 n n 
C2' "H2'A" IM5 sing 197 n n 
O3' C3' IM5 sing 198 n n 
C3' C4' IM5 sing 199 n n 
C3' H3' IM5 sing 200 n n 
O3' HO3' IM5 sing 201 n n 
C6' C4' IM5 sing 202 n n 
C4' C5' IM5 sing 203 n n 
C4' H4' IM5 sing 204 n n 
C5' O5' IM5 sing 205 n n 
C5' H5' IM5 sing 206 n n 
C5' "H5'A" IM5 sing 207 n n 
O5' HO5' IM5 sing 208 n n 
C6' H6' IM5 sing 209 n n 
C6' "H6'A" IM5 sing 210 n n 
N7 HN7 IM5 sing 211 n n 
#
_atom_sites.entry_id                     3PHB 
_atom_sites.fract_transf_matrix[1][1]    0.003714 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000021 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019 
_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]    0.007805 
_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 E 1 290 1 IM5 IM5 . 
H 3 PO4 E 1 291 2 PO4 PO4 . 
I 3 PO4 E 1 292 8 PO4 PO4 . 
J 2 IM5 Q 1 290 1 IM5 IM5 . 
K 3 PO4 Q 1 291 2 PO4 PO4 . 
L 3 PO4 Q 1 292 11 PO4 PO4 . 
M 3 PO4 S 1 290 9 PO4 PO4 . 
N 2 IM5 S 1 291 1 IM5 IM5 . 
O 3 PO4 S 1 292 2 PO4 PO4 . 
P 3 PO4 T 1 290 10 PO4 PO4 . 
Q 2 IM5 T 1 291 1 IM5 IM5 . 
R 3 PO4 T 1 292 2 PO4 PO4 . 
S 2 IM5 U 1 290 1 IM5 IM5 . 
T 3 PO4 U 1 291 2 PO4 PO4 . 
U 3 PO4 Y 1 290 7 PO4 PO4 . 
V 3 PO4 Y 1 291 12 PO4 PO4 . 
W 2 IM5 Y 1 292 1 IM5 IM5 . 
X 3 PO4 Y 1 293 2 PO4 PO4 . 
Y 4 HOH E 1 293 6 HOH HOH . 
Y 4 HOH E 2 294 8 HOH HOH . 
Y 4 HOH E 3 295 15 HOH HOH . 
Y 4 HOH E 4 296 16 HOH HOH . 
Y 4 HOH E 5 297 38 HOH HOH . 
Y 4 HOH E 6 298 50 HOH HOH . 
Y 4 HOH E 7 299 58 HOH HOH . 
Y 4 HOH E 8 300 63 HOH HOH . 
Y 4 HOH E 9 301 64 HOH HOH . 
Y 4 HOH E 10 302 65 HOH HOH . 
Y 4 HOH E 11 303 66 HOH HOH . 
Y 4 HOH E 12 304 67 HOH HOH . 
Y 4 HOH E 13 305 69 HOH HOH . 
Y 4 HOH E 14 306 70 HOH HOH . 
Y 4 HOH E 15 307 71 HOH HOH . 
Y 4 HOH E 16 308 79 HOH HOH . 
Z 4 HOH Q 1 293 7 HOH HOH . 
Z 4 HOH Q 2 294 12 HOH HOH . 
Z 4 HOH Q 3 295 18 HOH HOH . 
Z 4 HOH Q 4 296 20 HOH HOH . 
Z 4 HOH Q 5 297 22 HOH HOH . 
Z 4 HOH Q 6 298 26 HOH HOH . 
Z 4 HOH Q 7 299 28 HOH HOH . 
Z 4 HOH Q 8 300 32 HOH HOH . 
Z 4 HOH Q 9 301 44 HOH HOH . 
Z 4 HOH Q 10 302 48 HOH HOH . 
Z 4 HOH Q 11 303 52 HOH HOH . 
Z 4 HOH Q 12 304 53 HOH HOH . 
Z 4 HOH Q 13 305 72 HOH HOH . 
Z 4 HOH Q 14 306 73 HOH HOH . 
Z 4 HOH Q 15 307 75 HOH HOH . 
Z 4 HOH Q 16 308 76 HOH HOH . 
Z 4 HOH Q 17 309 77 HOH HOH . 
Z 4 HOH Q 18 310 78 HOH HOH . 
AA 4 HOH S 1 293 1 HOH HOH . 
AA 4 HOH S 2 294 23 HOH HOH . 
AA 4 HOH S 3 295 27 HOH HOH . 
AA 4 HOH S 4 296 30 HOH HOH . 
AA 4 HOH S 5 297 34 HOH HOH . 
AA 4 HOH S 6 298 35 HOH HOH . 
AA 4 HOH S 7 299 43 HOH HOH . 
AA 4 HOH S 8 300 45 HOH HOH . 
AA 4 HOH S 9 301 54 HOH HOH . 
AA 4 HOH S 10 302 60 HOH HOH . 
AA 4 HOH S 11 303 61 HOH HOH . 
AA 4 HOH S 12 304 80 HOH HOH . 
AA 4 HOH S 13 305 81 HOH HOH . 
AA 4 HOH S 14 306 82 HOH HOH . 
AA 4 HOH S 15 307 92 HOH HOH . 
BA 4 HOH T 1 293 5 HOH HOH . 
BA 4 HOH T 2 294 17 HOH HOH . 
BA 4 HOH T 3 295 21 HOH HOH . 
BA 4 HOH T 4 296 24 HOH HOH . 
BA 4 HOH T 5 297 33 HOH HOH . 
BA 4 HOH T 6 298 36 HOH HOH . 
BA 4 HOH T 7 299 51 HOH HOH . 
BA 4 HOH T 8 300 55 HOH HOH . 
BA 4 HOH T 9 301 83 HOH HOH . 
BA 4 HOH T 10 302 93 HOH HOH . 
CA 4 HOH U 1 292 3 HOH HOH . 
CA 4 HOH U 2 293 9 HOH HOH . 
CA 4 HOH U 3 294 10 HOH HOH . 
CA 4 HOH U 4 295 11 HOH HOH . 
CA 4 HOH U 5 296 31 HOH HOH . 
CA 4 HOH U 6 297 37 HOH HOH . 
CA 4 HOH U 7 298 40 HOH HOH . 
CA 4 HOH U 8 299 41 HOH HOH . 
CA 4 HOH U 9 300 42 HOH HOH . 
CA 4 HOH U 10 301 47 HOH HOH . 
CA 4 HOH U 11 302 56 HOH HOH . 
CA 4 HOH U 12 303 84 HOH HOH . 
CA 4 HOH U 13 304 85 HOH HOH . 
DA 4 HOH Y 1 294 2 HOH HOH . 
DA 4 HOH Y 2 295 4 HOH HOH . 
DA 4 HOH Y 3 296 13 HOH HOH . 
DA 4 HOH Y 4 297 19 HOH HOH . 
DA 4 HOH Y 5 298 25 HOH HOH . 
DA 4 HOH Y 6 299 29 HOH HOH . 
DA 4 HOH Y 7 300 49 HOH HOH . 
DA 4 HOH Y 8 301 57 HOH HOH . 
DA 4 HOH Y 9 302 59 HOH HOH . 
DA 4 HOH Y 10 303 68 HOH HOH . 
DA 4 HOH Y 11 304 74 HOH HOH . 
DA 4 HOH Y 12 305 87 HOH HOH . 
DA 4 HOH Y 13 306 88 HOH HOH . 
DA 4 HOH Y 14 307 89 HOH HOH . 
DA 4 HOH Y 15 308 90 HOH HOH . 
DA 4 HOH Y 16 309 91 HOH HOH . 
DA 4 HOH Y 17 310 94 HOH HOH . 
DA 4 HOH Y 18 311 95 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 . . . J 2 -30.59 6.197 -27.767 1 32.96 ? N1 IM5 290 Q 1 
HETATM 2 C C2 IM5 . . . J 2 -29.617 5.37 -27.314 1 32.15 ? C2 IM5 290 Q 1 
HETATM 3 N N2 IM5 . . . J 2 -29.648 4.981 -26.011 1 32.57 ? N2 IM5 290 Q 1 
HETATM 4 N N3 IM5 . . . J 2 -28.624 4.911 -28.115 1 30.22 ? N3 IM5 290 Q 1 
HETATM 5 C C4 IM5 . . . J 2 -28.581 5.261 -29.408 1 30.99 ? C4 IM5 290 Q 1 
HETATM 6 C C5 IM5 . . . J 2 -29.575 6.172 -29.968 1 33.07 ? C5 IM5 290 Q 1 
HETATM 7 C C6 IM5 . . . J 2 -30.627 6.628 -29.029 1 33.36 ? C6 IM5 290 Q 1 
HETATM 8 O O6 IM5 . . . J 2 -31.524 7.398 -29.4 1 37.86 ? O6 IM5 290 Q 1 
HETATM 9 N N7 IM5 . . . J 2 -29.245 6.365 -31.256 1 33.38 ? N7 IM5 290 Q 1 
HETATM 10 C C8 IM5 . . . J 2 -28.126 5.652 -31.583 1 33.02 ? C8 IM5 290 Q 1 
HETATM 11 C C9 IM5 . . . J 2 -27.637 4.942 -30.498 1 30.74 ? C9 IM5 290 Q 1 
HETATM 12 N N1' IM5 . . . J 2 -26.666 2.602 -30.709 1 27.73 ? N1' IM5 290 Q 1 
HETATM 13 C C10 IM5 . . . J 2 -26.408 4.068 -30.497 1 31.19 ? C10 IM5 290 Q 1 
HETATM 14 C C2' IM5 . . . J 2 -27.271 1.999 -29.542 1 26.15 ? C2' IM5 290 Q 1 
HETATM 15 C C3' IM5 . . . J 2 -27.726 0.638 -30.105 1 29.08 ? C3' IM5 290 Q 1 
HETATM 16 O O3' IM5 . . . J 2 -26.604 -0.23 -30.158 1 27.12 ? O3' IM5 290 Q 1 
HETATM 17 C C4' IM5 . . . J 2 -28.155 0.92 -31.527 1 29.29 ? C4' IM5 290 Q 1 
HETATM 18 C C5' IM5 . . . J 2 -29.664 0.971 -31.675 1 30.46 ? C5' IM5 290 Q 1 
HETATM 19 O O5' IM5 . . . J 2 -29.97 1.223 -33.049 1 37 ? O5' IM5 290 Q 1 
HETATM 20 C C6' IM5 . . . J 2 -27.537 2.275 -31.855 1 27.01 ? C6' IM5 290 Q 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    69 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           20 
#