data_2DPT
#
_model_server_result.job_id            YJiEdZoJUdkD1pQsvbtYgA 
_model_server_result.datetime_utc      '2024-11-23 07:16:52' 
_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          2dpt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1501}' 
#
_entry.id    2DPT 
#
_exptl.entry_id    2DPT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              471.51 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            PUROMYCIN 
_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            2DPT 
_cell.length_a            115.662 
_cell.length_b            129.139 
_cell.length_c            38.571 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2DPT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 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 C N N 
? 2 E N N 
#
_chem_comp.formula           'C22 H29 N7 O5' 
_chem_comp.formula_weight    471.51 
_chem_comp.id                PUY 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              PUROMYCIN 
_chem_comp.type              'rna 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 PUY sing 277 n n 
N HN1 PUY sing 278 n n 
N HN2 PUY sing 279 n n 
CA CB PUY sing 280 n n 
CA C PUY sing 281 n n 
CA HA PUY sing 282 n n 
CB CG PUY sing 283 n n 
CB HB1 PUY sing 284 n n 
CB HB2 PUY sing 285 n n 
CG CD1 PUY doub 286 n y 
CG CD2 PUY sing 287 n y 
CD1 CE1 PUY sing 288 n y 
CD1 HD1 PUY sing 289 n n 
CD2 CE2 PUY doub 290 n y 
CD2 HD2 PUY sing 291 n n 
CE1 CZ PUY doub 292 n y 
CE1 HE1 PUY sing 293 n n 
CE2 CZ PUY sing 294 n y 
CE2 HE2 PUY sing 295 n n 
CZ OM PUY sing 296 n n 
O C PUY doub 297 n n 
OM CMZ PUY sing 298 n n 
CMZ HMZ1 PUY sing 299 n n 
CMZ HMZ2 PUY sing 300 n n 
CMZ HMZ3 PUY sing 301 n n 
C N3' PUY sing 302 n n 
O5' C5' PUY sing 303 n n 
O5' H5' PUY sing 304 n n 
C5' C4' PUY sing 305 n n 
C5' "H5'1" PUY sing 306 n n 
C5' "H5''" PUY sing 307 n n 
C4' O4' PUY sing 308 n n 
C4' C3' PUY sing 309 n n 
C4' H4' PUY sing 310 n n 
O4' C1' PUY sing 311 n n 
C1' N9 PUY sing 312 n n 
C1' C2' PUY sing 313 n n 
C1' H1' PUY sing 314 n n 
N9 C4 PUY sing 315 n y 
N9 C8 PUY sing 316 n y 
C4 N3 PUY doub 317 n y 
C4 C5 PUY sing 318 n y 
N3 C2 PUY sing 319 n y 
C2 N1 PUY doub 320 n y 
C2 H2 PUY sing 321 n n 
N1 C6 PUY sing 322 n y 
C6 N6 PUY sing 323 n n 
C6 C5 PUY doub 324 n y 
N6 C9 PUY sing 325 n n 
N6 C10 PUY sing 326 n n 
C9 H91 PUY sing 327 n n 
C9 H92 PUY sing 328 n n 
C9 H93 PUY sing 329 n n 
C10 H101 PUY sing 330 n n 
C10 H102 PUY sing 331 n n 
C10 H103 PUY sing 332 n n 
C5 N7 PUY sing 333 n y 
N7 C8 PUY doub 334 n y 
C8 H8 PUY sing 335 n n 
C2' O2' PUY sing 336 n n 
C2' C3' PUY sing 337 n n 
C2' H2' PUY sing 338 n n 
O2' H1 PUY sing 339 n n 
C3' N3' PUY sing 340 n n 
C3' H3' PUY sing 341 n n 
N3' H3 PUY sing 342 n n 
#
_atom_sites.entry_id                     2DPT 
_atom_sites.fract_transf_matrix[1][1]    0.008646 
_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]    0.007744 
_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]    0.025926 
_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
C 2 PUY A 1 501 501 PUY PUC . 
D 3 TAR A 1 502 502 TAR TAR . 
E 2 PUY B 1 1501 501 PUY PUC . 
F 3 TAR B 1 1502 502 TAR TAR . 
G 4 HOH A 1 1002 1002 HOH HOH . 
G 4 HOH A 2 1003 1003 HOH HOH . 
G 4 HOH A 3 1004 1004 HOH HOH . 
G 4 HOH A 4 1008 1008 HOH HOH . 
G 4 HOH A 5 1009 1009 HOH HOH . 
G 4 HOH A 6 1010 1010 HOH HOH . 
G 4 HOH A 7 1011 1011 HOH HOH . 
G 4 HOH A 8 1013 1013 HOH HOH . 
H 4 HOH B 1 1001 1001 HOH HOH . 
H 4 HOH B 2 1005 1005 HOH HOH . 
H 4 HOH B 3 1006 1006 HOH HOH . 
H 4 HOH B 4 1007 1007 HOH HOH . 
H 4 HOH B 5 1012 1012 HOH HOH . 
H 4 HOH B 6 1014 1014 HOH HOH . 
H 4 HOH B 7 1015 1015 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 PUY . . . E 2 11.211 19.231 19.461 1 91.45 ? N PUY 1501 B 1 
HETATM 2 C CA PUY . . . E 2 12.365 19.853 18.741 1 90.23 ? CA PUY 1501 B 1 
HETATM 3 C CB PUY . . . E 2 12.392 21.356 19.14 1 88.08 ? CB PUY 1501 B 1 
HETATM 4 C CG PUY . . . E 2 11.693 22.324 18.197 1 86.49 ? CG PUY 1501 B 1 
HETATM 5 C CD1 PUY . . . E 2 11.409 23.643 18.607 1 86.45 ? CD1 PUY 1501 B 1 
HETATM 6 C CD2 PUY . . . E 2 11.306 21.924 16.866 1 85.32 ? CD2 PUY 1501 B 1 
HETATM 7 C CE1 PUY . . . E 2 10.767 24.56 17.754 1 86.08 ? CE1 PUY 1501 B 1 
HETATM 8 C CE2 PUY . . . E 2 10.651 22.861 15.998 1 83.97 ? CE2 PUY 1501 B 1 
HETATM 9 C CZ PUY . . . E 2 10.375 24.178 16.421 1 84.93 ? CZ PUY 1501 B 1 
HETATM 10 O O PUY . . . E 2 14.689 19.292 18.548 1 92.58 ? O PUY 1501 B 1 
HETATM 11 O OM PUY . . . E 2 9.763 25.172 15.715 1 84.69 ? OM PUY 1501 B 1 
HETATM 12 C CMZ PUY . . . E 2 10.378 25.64 14.507 1 84.65 ? CMZ PUY 1501 B 1 
HETATM 13 C C PUY . . . E 2 13.638 19.15 19.152 1 91.78 ? C PUY 1501 B 1 
HETATM 14 O O5' PUY . . . E 2 14.026 14.558 21.927 1 95.71 ? O5' PUY 1501 B 1 
HETATM 15 C C5' PUY . . . E 2 13.237 15.719 22.099 1 96.23 ? C5' PUY 1501 B 1 
HETATM 16 C C4' PUY . . . E 2 14.049 16.981 22.204 1 95.75 ? C4' PUY 1501 B 1 
HETATM 17 O O4' PUY . . . E 2 15.256 16.725 22.951 1 95.75 ? O4' PUY 1501 B 1 
HETATM 18 C C1' PUY . . . E 2 16.315 17.522 22.469 1 96.21 ? C1' PUY 1501 B 1 
HETATM 19 N N9 PUY . . . E 2 17.471 16.653 22.081 1 95.67 ? N9 PUY 1501 B 1 
HETATM 20 C C4 PUY . . . E 2 17.818 15.449 22.68 1 95.03 ? C4 PUY 1501 B 1 
HETATM 21 N N3 PUY . . . E 2 17.128 14.871 23.729 1 95.12 ? N3 PUY 1501 B 1 
HETATM 22 C C2 PUY . . . E 2 17.68 13.74 24.096 1 94.75 ? C2 PUY 1501 B 1 
HETATM 23 N N1 PUY . . . E 2 18.78 13.168 23.552 1 94.05 ? N1 PUY 1501 B 1 
HETATM 24 C C6 PUY . . . E 2 19.507 13.713 22.49 1 94.45 ? C6 PUY 1501 B 1 
HETATM 25 N N6 PUY . . . E 2 20.59 13.054 22.025 1 95.22 ? N6 PUY 1501 B 1 
HETATM 26 C C9 PUY . . . E 2 21.424 13.528 20.918 1 94.5 ? C9 PUY 1501 B 1 
HETATM 27 C C10 PUY . . . E 2 20.999 11.786 22.631 1 94.79 ? C10 PUY 1501 B 1 
HETATM 28 C C5 PUY . . . E 2 18.938 14.994 22.023 1 94.64 ? C5 PUY 1501 B 1 
HETATM 29 N N7 PUY . . . E 2 19.317 15.889 21.011 1 94.64 ? N7 PUY 1501 B 1 
HETATM 30 C C8 PUY . . . E 2 18.42 16.83 21.102 1 94.9 ? C8 PUY 1501 B 1 
HETATM 31 C C2' PUY . . . E 2 15.752 18.353 21.328 1 96.19 ? C2' PUY 1501 B 1 
HETATM 32 O O2' PUY . . . E 2 15.421 19.628 21.868 1 98.94 ? O2' PUY 1501 B 1 
HETATM 33 C C3' PUY . . . E 2 14.551 17.55 20.871 1 95.23 ? C3' PUY 1501 B 1 
HETATM 34 N N3' PUY . . . E 2 13.478 18.369 20.237 1 93.17 ? N3' PUY 1501 B 1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           34 
#