data_2DPT
#
_model_server_result.job_id            IXhkOy8Kf63K-_jbVxTf5w 
_model_server_result.datetime_utc      '2024-11-27 00:02:45' 
_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":"C","auth_seq_id":501}' 
#
_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 . . . C 2 37.02 55.243 10.588 1 89.63 ? N PUY 501 A 1 
HETATM 2 C CA PUY . . . C 2 35.923 55.562 9.632 1 88.58 ? CA PUY 501 A 1 
HETATM 3 C CB PUY . . . C 2 34.81 54.509 9.84 1 87.13 ? CB PUY 501 A 1 
HETATM 4 C CG PUY . . . C 2 34.752 53.344 8.879 1 86.16 ? CG PUY 501 A 1 
HETATM 5 C CD1 PUY . . . C 2 34.034 52.183 9.227 1 86.08 ? CD1 PUY 501 A 1 
HETATM 6 C CD2 PUY . . . C 2 35.409 53.383 7.606 1 84.65 ? CD2 PUY 501 A 1 
HETATM 7 C CE1 PUY . . . C 2 33.949 51.078 8.365 1 85.1 ? CE1 PUY 501 A 1 
HETATM 8 C CE2 PUY . . . C 2 35.322 52.254 6.728 1 84 ? CE2 PUY 501 A 1 
HETATM 9 C CZ PUY . . . C 2 34.6 51.099 7.087 1 84.67 ? CZ PUY 501 A 1 
HETATM 10 O O PUY . . . C 2 34.587 57.478 9.191 1 90.66 ? O PUY 501 A 1 
HETATM 11 O OM PUY . . . C 2 34.433 49.96 6.359 1 85.58 ? OM PUY 501 A 1 
HETATM 12 C CMZ PUY . . . C 2 34.006 50.063 4.991 1 86.19 ? CMZ PUY 501 A 1 
HETATM 13 C C PUY . . . C 2 35.395 56.937 9.93 1 89.94 ? C PUY 501 A 1 
HETATM 14 O O5' PUY . . . C 2 37.494 60.825 13.688 1 94.41 ? O5' PUY 501 A 1 
HETATM 15 C C5' PUY . . . C 2 37.422 59.488 13.23 1 94.22 ? C5' PUY 501 A 1 
HETATM 16 C C4' PUY . . . C 2 36.02 58.975 13.07 1 92.23 ? C4' PUY 501 A 1 
HETATM 17 O O4' PUY . . . C 2 35.101 59.902 13.674 1 92.26 ? O4' PUY 501 A 1 
HETATM 18 C C1' PUY . . . C 2 33.902 59.961 12.948 1 92.11 ? C1' PUY 501 A 1 
HETATM 19 N N9 PUY . . . C 2 33.509 61.357 12.592 1 90.17 ? N9 PUY 501 A 1 
HETATM 20 C C4 PUY . . . C 2 33.918 62.517 13.236 1 89.28 ? C4 PUY 501 A 1 
HETATM 21 N N3 PUY . . . C 2 34.787 62.553 14.313 1 88.62 ? N3 PUY 501 A 1 
HETATM 22 C C2 PUY . . . C 2 34.988 63.787 14.713 1 88.29 ? C2 PUY 501 A 1 
HETATM 23 N N1 PUY . . . C 2 34.449 64.909 14.178 1 88.18 ? N1 PUY 501 A 1 
HETATM 24 C C6 PUY . . . C 2 33.57 64.915 13.087 1 87.59 ? C6 PUY 501 A 1 
HETATM 25 N N6 PUY . . . C 2 33.09 66.092 12.636 1 87.53 ? N6 PUY 501 A 1 
HETATM 26 C C9 PUY . . . C 2 32.171 66.217 11.508 1 86.32 ? C9 PUY 501 A 1 
HETATM 27 C C10 PUY . . . C 2 33.48 67.344 13.277 1 87.38 ? C10 PUY 501 A 1 
HETATM 28 C C5 PUY . . . C 2 33.303 63.561 12.588 1 88.16 ? C5 PUY 501 A 1 
HETATM 29 N N7 PUY . . . C 2 32.499 63.087 11.537 1 88.21 ? N7 PUY 501 A 1 
HETATM 30 C C8 PUY . . . C 2 32.669 61.799 11.603 1 88.64 ? C8 PUY 501 A 1 
HETATM 31 C C2' PUY . . . C 2 34.04 59.032 11.771 1 92.64 ? C2' PUY 501 A 1 
HETATM 32 O O2' PUY . . . C 2 33.336 57.847 12.124 1 95.61 ? O2' PUY 501 A 1 
HETATM 33 C C3' PUY . . . C 2 35.533 58.833 11.621 1 91.92 ? C3' PUY 501 A 1 
HETATM 34 N N3' PUY . . . C 2 35.894 57.481 11.08 1 90.86 ? N3' PUY 501 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           281 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           34 
#