data_4TVA
#
_model_server_result.job_id            vwik8hUcalRwtCO7MNIgDw 
_model_server_result.datetime_utc      '2024-11-13 04:36:53' 
_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          4tva 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":801}' 
#
_entry.id    4TVA 
#
_exptl.entry_id    4TVA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              471.51 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            PUROMYCIN 
_entity.pdbx_number_of_molecules    1 
_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            4TVA 
_cell.length_a            173.475 
_cell.length_b            173.475 
_cell.length_c            138.492 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4TVA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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                     4TVA 
_atom_sites.fract_transf_matrix[1][1]    0.005765 
_atom_sites.fract_transf_matrix[1][2]    0.003328 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006656 
_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]    0.007221 
_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 3 PHE A 1 401 1 PHE PHE . 
D 4 PUY B 1 801 1 PUY PUY . 
E 5 HOH A 1 501 118 HOH HOH . 
E 5 HOH A 2 502 29 HOH HOH . 
E 5 HOH A 3 503 165 HOH HOH . 
E 5 HOH A 4 504 116 HOH HOH . 
E 5 HOH A 5 505 81 HOH HOH . 
E 5 HOH A 6 506 2 HOH HOH . 
E 5 HOH A 7 507 9 HOH HOH . 
E 5 HOH A 8 508 15 HOH HOH . 
E 5 HOH A 9 509 22 HOH HOH . 
E 5 HOH A 10 510 35 HOH HOH . 
E 5 HOH A 11 511 37 HOH HOH . 
E 5 HOH A 12 512 43 HOH HOH . 
E 5 HOH A 13 513 48 HOH HOH . 
E 5 HOH A 14 514 49 HOH HOH . 
E 5 HOH A 15 515 56 HOH HOH . 
E 5 HOH A 16 516 62 HOH HOH . 
E 5 HOH A 17 517 66 HOH HOH . 
E 5 HOH A 18 518 68 HOH HOH . 
E 5 HOH A 19 519 69 HOH HOH . 
E 5 HOH A 20 520 76 HOH HOH . 
E 5 HOH A 21 521 78 HOH HOH . 
E 5 HOH A 22 522 91 HOH HOH . 
E 5 HOH A 23 523 107 HOH HOH . 
E 5 HOH A 24 524 126 HOH HOH . 
E 5 HOH A 25 525 131 HOH HOH . 
E 5 HOH A 26 526 148 HOH HOH . 
E 5 HOH A 27 527 149 HOH HOH . 
E 5 HOH A 28 528 153 HOH HOH . 
E 5 HOH A 29 529 172 HOH HOH . 
F 5 HOH B 1 901 127 HOH HOH . 
F 5 HOH B 2 902 88 HOH HOH . 
F 5 HOH B 3 903 67 HOH HOH . 
F 5 HOH B 4 904 168 HOH HOH . 
F 5 HOH B 5 905 175 HOH HOH . 
F 5 HOH B 6 906 47 HOH HOH . 
F 5 HOH B 7 907 70 HOH HOH . 
F 5 HOH B 8 908 141 HOH HOH . 
F 5 HOH B 9 909 24 HOH HOH . 
F 5 HOH B 10 910 51 HOH HOH . 
F 5 HOH B 11 911 6 HOH HOH . 
F 5 HOH B 12 912 169 HOH HOH . 
F 5 HOH B 13 913 18 HOH HOH . 
F 5 HOH B 14 914 106 HOH HOH . 
F 5 HOH B 15 915 38 HOH HOH . 
F 5 HOH B 16 916 93 HOH HOH . 
F 5 HOH B 17 917 60 HOH HOH . 
F 5 HOH B 18 918 162 HOH HOH . 
F 5 HOH B 19 919 146 HOH HOH . 
F 5 HOH B 20 920 114 HOH HOH . 
F 5 HOH B 21 921 142 HOH HOH . 
F 5 HOH B 22 922 144 HOH HOH . 
F 5 HOH B 23 923 161 HOH HOH . 
F 5 HOH B 24 924 110 HOH HOH . 
F 5 HOH B 25 925 1 HOH HOH . 
F 5 HOH B 26 926 3 HOH HOH . 
F 5 HOH B 27 927 4 HOH HOH . 
F 5 HOH B 28 928 5 HOH HOH . 
F 5 HOH B 29 929 7 HOH HOH . 
F 5 HOH B 30 930 8 HOH HOH . 
F 5 HOH B 31 931 10 HOH HOH . 
F 5 HOH B 32 932 11 HOH HOH . 
F 5 HOH B 33 933 12 HOH HOH . 
F 5 HOH B 34 934 13 HOH HOH . 
F 5 HOH B 35 935 14 HOH HOH . 
F 5 HOH B 36 936 16 HOH HOH . 
F 5 HOH B 37 937 17 HOH HOH . 
F 5 HOH B 38 938 19 HOH HOH . 
F 5 HOH B 39 939 20 HOH HOH . 
F 5 HOH B 40 940 21 HOH HOH . 
F 5 HOH B 41 941 23 HOH HOH . 
F 5 HOH B 42 942 25 HOH HOH . 
F 5 HOH B 43 943 26 HOH HOH . 
F 5 HOH B 44 944 27 HOH HOH . 
F 5 HOH B 45 945 28 HOH HOH . 
F 5 HOH B 46 946 30 HOH HOH . 
F 5 HOH B 47 947 31 HOH HOH . 
F 5 HOH B 48 948 32 HOH HOH . 
F 5 HOH B 49 949 33 HOH HOH . 
F 5 HOH B 50 950 34 HOH HOH . 
F 5 HOH B 51 951 36 HOH HOH . 
F 5 HOH B 52 952 39 HOH HOH . 
F 5 HOH B 53 953 40 HOH HOH . 
F 5 HOH B 54 954 41 HOH HOH . 
F 5 HOH B 55 955 42 HOH HOH . 
F 5 HOH B 56 956 44 HOH HOH . 
F 5 HOH B 57 957 45 HOH HOH . 
F 5 HOH B 58 958 46 HOH HOH . 
F 5 HOH B 59 959 50 HOH HOH . 
F 5 HOH B 60 960 52 HOH HOH . 
F 5 HOH B 61 961 53 HOH HOH . 
F 5 HOH B 62 962 54 HOH HOH . 
F 5 HOH B 63 963 55 HOH HOH . 
F 5 HOH B 64 964 57 HOH HOH . 
F 5 HOH B 65 965 58 HOH HOH . 
F 5 HOH B 66 966 59 HOH HOH . 
F 5 HOH B 67 967 61 HOH HOH . 
F 5 HOH B 68 968 63 HOH HOH . 
F 5 HOH B 69 969 64 HOH HOH . 
F 5 HOH B 70 970 65 HOH HOH . 
F 5 HOH B 71 971 71 HOH HOH . 
F 5 HOH B 72 972 72 HOH HOH . 
F 5 HOH B 73 973 73 HOH HOH . 
F 5 HOH B 74 974 74 HOH HOH . 
F 5 HOH B 75 975 75 HOH HOH . 
F 5 HOH B 76 976 77 HOH HOH . 
F 5 HOH B 77 977 79 HOH HOH . 
F 5 HOH B 78 978 80 HOH HOH . 
F 5 HOH B 79 979 82 HOH HOH . 
F 5 HOH B 80 980 83 HOH HOH . 
F 5 HOH B 81 981 84 HOH HOH . 
F 5 HOH B 82 982 85 HOH HOH . 
F 5 HOH B 83 983 86 HOH HOH . 
F 5 HOH B 84 984 87 HOH HOH . 
F 5 HOH B 85 985 89 HOH HOH . 
F 5 HOH B 86 986 90 HOH HOH . 
F 5 HOH B 87 987 92 HOH HOH . 
F 5 HOH B 88 988 94 HOH HOH . 
F 5 HOH B 89 989 95 HOH HOH . 
F 5 HOH B 90 990 96 HOH HOH . 
F 5 HOH B 91 991 97 HOH HOH . 
F 5 HOH B 92 992 98 HOH HOH . 
F 5 HOH B 93 993 99 HOH HOH . 
F 5 HOH B 94 994 100 HOH HOH . 
F 5 HOH B 95 995 101 HOH HOH . 
F 5 HOH B 96 996 102 HOH HOH . 
F 5 HOH B 97 997 103 HOH HOH . 
F 5 HOH B 98 998 104 HOH HOH . 
F 5 HOH B 99 999 105 HOH HOH . 
F 5 HOH B 100 1000 108 HOH HOH . 
F 5 HOH B 101 1001 109 HOH HOH . 
F 5 HOH B 102 1002 111 HOH HOH . 
F 5 HOH B 103 1003 112 HOH HOH . 
F 5 HOH B 104 1004 113 HOH HOH . 
F 5 HOH B 105 1005 115 HOH HOH . 
F 5 HOH B 106 1006 117 HOH HOH . 
F 5 HOH B 107 1007 119 HOH HOH . 
F 5 HOH B 108 1008 120 HOH HOH . 
F 5 HOH B 109 1009 121 HOH HOH . 
F 5 HOH B 110 1010 122 HOH HOH . 
F 5 HOH B 111 1011 123 HOH HOH . 
F 5 HOH B 112 1012 124 HOH HOH . 
F 5 HOH B 113 1013 125 HOH HOH . 
F 5 HOH B 114 1014 128 HOH HOH . 
F 5 HOH B 115 1015 129 HOH HOH . 
F 5 HOH B 116 1016 130 HOH HOH . 
F 5 HOH B 117 1017 132 HOH HOH . 
F 5 HOH B 118 1018 133 HOH HOH . 
F 5 HOH B 119 1019 134 HOH HOH . 
F 5 HOH B 120 1020 135 HOH HOH . 
F 5 HOH B 121 1021 136 HOH HOH . 
F 5 HOH B 122 1022 137 HOH HOH . 
F 5 HOH B 123 1023 138 HOH HOH . 
F 5 HOH B 124 1024 139 HOH HOH . 
F 5 HOH B 125 1025 140 HOH HOH . 
F 5 HOH B 126 1026 143 HOH HOH . 
F 5 HOH B 127 1027 145 HOH HOH . 
F 5 HOH B 128 1028 147 HOH HOH . 
F 5 HOH B 129 1029 150 HOH HOH . 
F 5 HOH B 130 1030 151 HOH HOH . 
F 5 HOH B 131 1031 152 HOH HOH . 
F 5 HOH B 132 1032 154 HOH HOH . 
F 5 HOH B 133 1033 155 HOH HOH . 
F 5 HOH B 134 1034 156 HOH HOH . 
F 5 HOH B 135 1035 157 HOH HOH . 
F 5 HOH B 136 1036 158 HOH HOH . 
F 5 HOH B 137 1037 159 HOH HOH . 
F 5 HOH B 138 1038 160 HOH HOH . 
F 5 HOH B 139 1039 163 HOH HOH . 
F 5 HOH B 140 1040 164 HOH HOH . 
F 5 HOH B 141 1041 166 HOH HOH . 
F 5 HOH B 142 1042 167 HOH HOH . 
F 5 HOH B 143 1043 170 HOH HOH . 
F 5 HOH B 144 1044 171 HOH HOH . 
F 5 HOH B 145 1045 173 HOH HOH . 
F 5 HOH B 146 1046 174 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 . . . D 4 3.311 88.223 37.149 1 80.6 ? N PUY 801 B 1 
HETATM 2 C CA PUY . . . D 4 2.36 87.085 37.179 1 81.69 ? CA PUY 801 B 1 
HETATM 3 C CB PUY . . . D 4 3.201 85.863 37.6 1 79.81 ? CB PUY 801 B 1 
HETATM 4 C CG PUY . . . D 4 3.643 85.7 39.052 1 78.48 ? CG PUY 801 B 1 
HETATM 5 C CD1 PUY . . . D 4 4.913 86.076 39.424 1 78.37 ? CD1 PUY 801 B 1 
HETATM 6 C CD2 PUY . . . D 4 2.716 85.087 39.851 1 77.76 ? CD2 PUY 801 B 1 
HETATM 7 C CE1 PUY . . . D 4 5.309 85.818 40.77 1 76.62 ? CE1 PUY 801 B 1 
HETATM 8 C CE2 PUY . . . D 4 3.08 84.822 41.196 1 75.16 ? CE2 PUY 801 B 1 
HETATM 9 C CZ PUY . . . D 4 4.389 85.188 41.66 1 76.32 ? CZ PUY 801 B 1 
HETATM 10 O O PUY . . . D 4 0.179 87.956 37.133 1 80.64 ? O PUY 801 B 1 
HETATM 11 O OM PUY . . . D 4 4.721 84.908 42.984 1 77.2 ? OM PUY 801 B 1 
HETATM 12 C CMZ PUY . . . D 4 3.891 84.291 43.953 1 76.63 ? CMZ PUY 801 B 1 
HETATM 13 C C PUY . . . D 4 1.04 87.486 37.836 1 83.54 ? C PUY 801 B 1 
HETATM 14 O O5' PUY . . . D 4 -0.053 83.734 39.932 1 92.01 ? O5' PUY 801 B 1 
HETATM 15 C C5' PUY . . . D 4 -0.39 83.939 38.579 1 90.95 ? C5' PUY 801 B 1 
HETATM 16 C C4' PUY . . . D 4 -0.737 85.416 38.347 1 91.08 ? C4' PUY 801 B 1 
HETATM 17 O O4' PUY . . . D 4 -2.121 85.47 38.136 1 93.23 ? O4' PUY 801 B 1 
HETATM 18 C C1' PUY . . . D 4 -2.624 86.725 38.521 1 94.94 ? C1' PUY 801 B 1 
HETATM 19 N N9 PUY . . . D 4 -4.023 86.503 38.711 1 98.5 ? N9 PUY 801 B 1 
HETATM 20 C C4 PUY . . . D 4 -4.849 86.662 39.9 1 100 ? C4 PUY 801 B 1 
HETATM 21 N N3 PUY . . . D 4 -4.655 87.213 41.234 1 99.95 ? N3 PUY 801 B 1 
HETATM 22 C C2 PUY . . . D 4 -5.664 87.218 42.182 1 99.65 ? C2 PUY 801 B 1 
HETATM 23 N N1 PUY . . . D 4 -6.943 86.671 41.9 1 100 ? N1 PUY 801 B 1 
HETATM 24 C C6 PUY . . . D 4 -7.267 86.087 40.613 1 100 ? C6 PUY 801 B 1 
HETATM 25 N N6 PUY . . . D 4 -8.687 85.498 40.373 1 100 ? N6 PUY 801 B 1 
HETATM 26 C C9 PUY . . . D 4 -9.709 85.533 41.451 1 100.5 ? C9 PUY 801 B 1 
HETATM 27 C C10 PUY . . . D 4 -9.07 84.903 39.135 1 99.69 ? C10 PUY 801 B 1 
HETATM 28 C C5 PUY . . . D 4 -6.159 86.093 39.557 1 100 ? C5 PUY 801 B 1 
HETATM 29 N N7 PUY . . . D 4 -6.088 85.631 38.206 1 100 ? N7 PUY 801 B 1 
HETATM 30 C C8 PUY . . . D 4 -4.812 85.89 37.734 1 99.06 ? C8 PUY 801 B 1 
HETATM 31 C C2' PUY . . . D 4 -1.771 87.141 39.716 1 92.59 ? C2' PUY 801 B 1 
HETATM 32 O O2' PUY . . . D 4 -1.608 88.531 39.778 1 90.34 ? O2' PUY 801 B 1 
HETATM 33 C C3' PUY . . . D 4 -0.432 86.424 39.467 1 90.07 ? C3' PUY 801 B 1 
HETATM 34 N N3' PUY . . . D 4 0.795 87.19 39.166 1 86.37 ? N3' PUY 801 B 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           34 
#