data_5NC5
#
_model_server_result.job_id            F5OC2Ju-FKVQOHLqZLeiGQ 
_model_server_result.datetime_utc      '2024-11-22 13:36:32' 
_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          5nc5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"PA","auth_seq_id":1120}' 
#
_entry.id    5NC5 
#
_exptl.entry_id    5NC5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              471.51 
_entity.id                          8 
_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         90 
_cell.entry_id            5NC5 
_cell.length_a            147.245 
_cell.length_b            167.646 
_cell.length_c            249.98 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5NC5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB,BB,CB,DB,EB,FB,GB,HB,IB,JB,KB,LB,MB 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      8 
_struct_asym.id                             PA 
_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 474 n n 
N HN1 PUY sing 475 n n 
N HN2 PUY sing 476 n n 
CA CB PUY sing 477 n n 
CA C PUY sing 478 n n 
CA HA PUY sing 479 n n 
CB CG PUY sing 480 n n 
CB HB1 PUY sing 481 n n 
CB HB2 PUY sing 482 n n 
CG CD1 PUY doub 483 n y 
CG CD2 PUY sing 484 n y 
CD1 CE1 PUY sing 485 n y 
CD1 HD1 PUY sing 486 n n 
CD2 CE2 PUY doub 487 n y 
CD2 HD2 PUY sing 488 n n 
CE1 CZ PUY doub 489 n y 
CE1 HE1 PUY sing 490 n n 
CE2 CZ PUY sing 491 n y 
CE2 HE2 PUY sing 492 n n 
CZ OM PUY sing 493 n n 
O C PUY doub 494 n n 
OM CMZ PUY sing 495 n n 
CMZ HMZ1 PUY sing 496 n n 
CMZ HMZ2 PUY sing 497 n n 
CMZ HMZ3 PUY sing 498 n n 
C N3' PUY sing 499 n n 
O5' C5' PUY sing 500 n n 
O5' H5' PUY sing 501 n n 
C5' C4' PUY sing 502 n n 
C5' "H5'1" PUY sing 503 n n 
C5' "H5''" PUY sing 504 n n 
C4' O4' PUY sing 505 n n 
C4' C3' PUY sing 506 n n 
C4' H4' PUY sing 507 n n 
O4' C1' PUY sing 508 n n 
C1' N9 PUY sing 509 n n 
C1' C2' PUY sing 510 n n 
C1' H1' PUY sing 511 n n 
N9 C4 PUY sing 512 n y 
N9 C8 PUY sing 513 n y 
C4 N3 PUY doub 514 n y 
C4 C5 PUY sing 515 n y 
N3 C2 PUY sing 516 n y 
C2 N1 PUY doub 517 n y 
C2 H2 PUY sing 518 n n 
N1 C6 PUY sing 519 n y 
C6 N6 PUY sing 520 n n 
C6 C5 PUY doub 521 n y 
N6 C9 PUY sing 522 n n 
N6 C10 PUY sing 523 n n 
C9 H91 PUY sing 524 n n 
C9 H92 PUY sing 525 n n 
C9 H93 PUY sing 526 n n 
C10 H101 PUY sing 527 n n 
C10 H102 PUY sing 528 n n 
C10 H103 PUY sing 529 n n 
C5 N7 PUY sing 530 n y 
N7 C8 PUY doub 531 n y 
C8 H8 PUY sing 532 n n 
C2' O2' PUY sing 533 n n 
C2' C3' PUY sing 534 n n 
C2' H2' PUY sing 535 n n 
O2' H1 PUY sing 536 n n 
C3' N3' PUY sing 537 n n 
C3' H3' PUY sing 538 n n 
N3' H3 PUY sing 539 n n 
#
_atom_sites.entry_id                     5NC5 
_atom_sites.fract_transf_matrix[1][1]    0.006791 
_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]    0.005965 
_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]    0.004 
_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
I 4 LMT A 1 1101 1101 LMT LMT . 
J 4 LMT A 1 1102 1103 LMT LMT . 
K 5 D12 A 1 1103 1106 D12 D12 . 
L 6 D10 A 1 1104 1108 D10 D10 . 
M 6 D10 A 1 1105 1109 D10 D10 . 
N 6 D10 A 1 1106 1113 D10 D10 . 
O 7 DD9 A 1 1107 1116 DD9 D10 . 
P 6 D10 A 1 1108 1120 D10 D10 . 
Q 6 D10 A 1 1109 1132 D10 D10 . 
R 7 DD9 A 1 1110 1135 DD9 D10 . 
S 4 LMT A 1 1111 1101 LMT LMT . 
T 5 D12 A 1 1112 1107 D12 D12 . 
U 7 DD9 A 1 1113 1142 DD9 D10 . 
V 7 DD9 A 1 1114 1146 DD9 D10 . 
W 6 D10 B 1 1101 1111 D10 D10 . 
X 7 DD9 B 1 1102 1133 DD9 D10 . 
Y 6 D10 B 1 1103 1105 D10 D10 . 
Z 5 D12 B 1 1104 1108 D12 D12 . 
AA 6 D10 B 1 1105 1109 D10 D10 . 
BA 7 DD9 B 1 1106 1114 DD9 D10 . 
CA 7 DD9 B 1 1107 1115 DD9 D10 . 
DA 6 D10 B 1 1108 1117 D10 D10 . 
EA 7 DD9 B 1 1109 1118 DD9 D10 . 
FA 6 D10 B 1 1110 1119 D10 D10 . 
GA 6 D10 B 1 1111 1121 D10 D10 . 
HA 7 DD9 B 1 1112 1122 DD9 D10 . 
IA 6 D10 B 1 1113 1123 D10 D10 . 
JA 6 D10 B 1 1114 1127 D10 D10 . 
KA 7 DD9 B 1 1115 1134 DD9 D10 . 
LA 6 D10 B 1 1116 1138 D10 D10 . 
MA 6 D10 B 1 1117 1139 D10 D10 . 
NA 6 D10 B 1 1118 1140 D10 D10 . 
OA 7 DD9 B 1 1119 1141 DD9 D10 . 
PA 8 PUY B 1 1120 6409 PUY PUY . 
QA 5 D12 B 1 1121 1110 D12 D12 . 
RA 6 D10 B 1 1122 1129 D10 D10 . 
SA 7 DD9 C 1 1101 1136 DD9 D10 . 
TA 6 D10 C 1 1102 1137 D10 D10 . 
UA 5 D12 C 1 1103 1102 D12 D12 . 
VA 6 D10 C 1 1104 1104 D10 D10 . 
WA 9 HEX C 1 1105 1105 HEX HEX . 
XA 5 D12 C 1 1106 1106 D12 D12 . 
YA 5 D12 C 1 1107 1109 D12 D12 . 
ZA 5 D12 C 1 1108 1111 D12 D12 . 
AB 7 DD9 C 1 1109 1124 DD9 D10 . 
BB 7 DD9 C 1 1110 1125 DD9 D10 . 
CB 6 D10 C 1 1111 1126 D10 D10 . 
DB 6 D10 C 1 1112 1128 D10 D10 . 
EB 6 D10 C 1 1113 1130 D10 D10 . 
FB 6 D10 C 1 1114 1131 D10 D10 . 
GB 6 D10 C 1 1115 1143 D10 D10 . 
HB 6 D10 C 1 1116 1144 D10 D10 . 
IB 6 D10 C 1 1117 1145 D10 D10 . 
JB 10 HOH A 1 1201 1555 HOH HOH . 
JB 10 HOH A 2 1202 1571 HOH HOH . 
JB 10 HOH A 3 1203 1534 HOH HOH . 
JB 10 HOH A 4 1204 1510 HOH HOH . 
JB 10 HOH A 5 1205 1551 HOH HOH . 
JB 10 HOH A 6 1206 1592 HOH HOH . 
JB 10 HOH A 7 1207 1502 HOH HOH . 
JB 10 HOH A 8 1208 1599 HOH HOH . 
JB 10 HOH A 9 1209 1537 HOH HOH . 
JB 10 HOH A 10 1210 1591 HOH HOH . 
JB 10 HOH A 11 1211 1588 HOH HOH . 
JB 10 HOH A 12 1212 1549 HOH HOH . 
JB 10 HOH A 13 1213 1582 HOH HOH . 
JB 10 HOH A 14 1214 1535 HOH HOH . 
JB 10 HOH A 15 1215 1536 HOH HOH . 
JB 10 HOH A 16 1216 1511 HOH HOH . 
JB 10 HOH A 17 1217 1581 HOH HOH . 
JB 10 HOH A 18 1218 1580 HOH HOH . 
JB 10 HOH A 19 1219 1541 HOH HOH . 
JB 10 HOH A 20 1220 1543 HOH HOH . 
JB 10 HOH A 21 1221 1542 HOH HOH . 
JB 10 HOH A 22 1222 1594 HOH HOH . 
JB 10 HOH A 23 1223 1596 HOH HOH . 
JB 10 HOH A 24 1224 1504 HOH HOH . 
JB 10 HOH A 25 1225 1507 HOH HOH . 
JB 10 HOH A 26 1226 1554 HOH HOH . 
JB 10 HOH A 27 1227 1587 HOH HOH . 
JB 10 HOH A 28 1228 1512 HOH HOH . 
JB 10 HOH A 29 1229 1579 HOH HOH . 
JB 10 HOH A 30 1230 1550 HOH HOH . 
JB 10 HOH A 31 1231 1563 HOH HOH . 
JB 10 HOH A 32 1232 1574 HOH HOH . 
JB 10 HOH A 33 1233 1568 HOH HOH . 
JB 10 HOH A 34 1234 1589 HOH HOH . 
JB 10 HOH A 35 1235 1577 HOH HOH . 
JB 10 HOH A 36 1236 1540 HOH HOH . 
JB 10 HOH A 37 1237 1595 HOH HOH . 
JB 10 HOH A 38 1238 1573 HOH HOH . 
JB 10 HOH A 39 1239 1584 HOH HOH . 
JB 10 HOH A 40 1240 1517 HOH HOH . 
JB 10 HOH A 41 1241 1539 HOH HOH . 
JB 10 HOH A 42 1242 1552 HOH HOH . 
JB 10 HOH A 43 1243 1575 HOH HOH . 
JB 10 HOH A 44 1244 1597 HOH HOH . 
JB 10 HOH A 45 1245 1590 HOH HOH . 
JB 10 HOH A 46 1246 1516 HOH HOH . 
JB 10 HOH A 47 1247 1576 HOH HOH . 
JB 10 HOH A 48 1248 1567 HOH HOH . 
JB 10 HOH A 49 1249 1593 HOH HOH . 
JB 10 HOH A 50 1250 1538 HOH HOH . 
KB 10 HOH B 1 1201 1559 HOH HOH . 
KB 10 HOH B 2 1202 1506 HOH HOH . 
KB 10 HOH B 3 1203 1569 HOH HOH . 
KB 10 HOH B 4 1204 1553 HOH HOH . 
KB 10 HOH B 5 1205 1533 HOH HOH . 
KB 10 HOH B 6 1206 1556 HOH HOH . 
KB 10 HOH B 7 1207 1557 HOH HOH . 
KB 10 HOH B 8 1208 1501 HOH HOH . 
KB 10 HOH B 9 1209 1562 HOH HOH . 
KB 10 HOH B 10 1210 1505 HOH HOH . 
KB 10 HOH B 11 1211 1558 HOH HOH . 
KB 10 HOH B 12 1212 1578 HOH HOH . 
KB 10 HOH B 13 1213 1564 HOH HOH . 
KB 10 HOH B 14 1214 1513 HOH HOH . 
KB 10 HOH B 15 1215 1561 HOH HOH . 
KB 10 HOH B 16 1216 1514 HOH HOH . 
KB 10 HOH B 17 1217 1544 HOH HOH . 
KB 10 HOH B 18 1218 1565 HOH HOH . 
KB 10 HOH B 19 1219 1548 HOH HOH . 
KB 10 HOH B 20 1220 1545 HOH HOH . 
KB 10 HOH B 21 1221 1508 HOH HOH . 
KB 10 HOH B 22 1222 1570 HOH HOH . 
KB 10 HOH B 23 1223 1546 HOH HOH . 
KB 10 HOH B 24 1224 1509 HOH HOH . 
KB 10 HOH B 25 1225 1515 HOH HOH . 
KB 10 HOH B 26 1226 1566 HOH HOH . 
LB 10 HOH C 1 1201 1522 HOH HOH . 
LB 10 HOH C 2 1202 1524 HOH HOH . 
LB 10 HOH C 3 1203 1531 HOH HOH . 
LB 10 HOH C 4 1204 1521 HOH HOH . 
LB 10 HOH C 5 1205 1528 HOH HOH . 
LB 10 HOH C 6 1206 1525 HOH HOH . 
LB 10 HOH C 7 1207 1572 HOH HOH . 
LB 10 HOH C 8 1208 1527 HOH HOH . 
LB 10 HOH C 9 1209 1530 HOH HOH . 
LB 10 HOH C 10 1210 1529 HOH HOH . 
LB 10 HOH C 11 1211 1583 HOH HOH . 
LB 10 HOH C 12 1212 1585 HOH HOH . 
LB 10 HOH C 13 1213 1519 HOH HOH . 
LB 10 HOH C 14 1214 1526 HOH HOH . 
LB 10 HOH C 15 1215 1523 HOH HOH . 
LB 10 HOH C 16 1216 1503 HOH HOH . 
LB 10 HOH C 17 1217 1520 HOH HOH . 
LB 10 HOH C 18 1218 1598 HOH HOH . 
LB 10 HOH C 19 1219 1586 HOH HOH . 
LB 10 HOH C 20 1220 1532 HOH HOH . 
LB 10 HOH C 21 1221 1518 HOH HOH . 
MB 10 HOH D 1 201 1547 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 . . . PA 8 24.166 -48.992 -50.718 1 200.26 ? N PUY 1120 B 1 
HETATM 2 C CA PUY . . . PA 8 24.427 -50.367 -50.964 1 193.99 ? CA PUY 1120 B 1 
HETATM 3 C CB PUY . . . PA 8 23.327 -50.81 -51.956 1 180.54 ? CB PUY 1120 B 1 
HETATM 4 C CG PUY . . . PA 8 21.908 -51.41 -51.69 1 167.31 ? CG PUY 1120 B 1 
HETATM 5 C CD1 PUY . . . PA 8 21.673 -52.502 -50.947 1 159.68 ? CD1 PUY 1120 B 1 
HETATM 6 C CD2 PUY . . . PA 8 20.804 -51.003 -52.435 1 151.59 ? CD2 PUY 1120 B 1 
HETATM 7 C CE1 PUY . . . PA 8 20.409 -53.084 -50.824 1 143.05 ? CE1 PUY 1120 B 1 
HETATM 8 C CE2 PUY . . . PA 8 19.509 -51.547 -52.354 1 137.55 ? CE2 PUY 1120 B 1 
HETATM 9 C CZ PUY . . . PA 8 19.324 -52.634 -51.539 1 129.59 ? CZ PUY 1120 B 1 
HETATM 10 O O PUY . . . PA 8 26.682 -49.906 -50.536 1 231.03 ? O PUY 1120 B 1 
HETATM 11 O OM PUY . . . PA 8 18.082 -53.296 -51.409 1 99.61 ? OM PUY 1120 B 1 
HETATM 12 C CMZ PUY . . . PA 8 18.035 -54.502 -50.709 1 96.7 ? CMZ PUY 1120 B 1 
HETATM 13 C C PUY . . . PA 8 25.987 -50.527 -51.202 1 207.11 ? C PUY 1120 B 1 
HETATM 14 O O5' PUY . . . PA 8 30.692 -50.226 -49.816 1 133.83 ? O5' PUY 1120 B 1 
HETATM 15 C C5' PUY . . . PA 8 29.374 -50.28 -50.185 1 151.48 ? C5' PUY 1120 B 1 
HETATM 16 C C4' PUY . . . PA 8 29.181 -50.303 -51.716 1 169.76 ? C4' PUY 1120 B 1 
HETATM 17 O O4' PUY . . . PA 8 30.283 -50.458 -52.466 1 168.31 ? O4' PUY 1120 B 1 
HETATM 18 C C1' PUY . . . PA 8 30.229 -51.789 -53.299 1 186.81 ? C1' PUY 1120 B 1 
HETATM 19 N N9 PUY . . . PA 8 31.262 -52.616 -52.764 1 176.91 ? N9 PUY 1120 B 1 
HETATM 20 C C4 PUY . . . PA 8 31.183 -53.327 -51.66 1 172.34 ? C4 PUY 1120 B 1 
HETATM 21 N N3 PUY . . . PA 8 30.12 -53.411 -50.831 1 175.41 ? N3 PUY 1120 B 1 
HETATM 22 C C2 PUY . . . PA 8 30.162 -54.186 -49.726 1 163.8 ? C2 PUY 1120 B 1 
HETATM 23 N N1 PUY . . . PA 8 31.291 -54.856 -49.449 1 150.31 ? N1 PUY 1120 B 1 
HETATM 24 C C6 PUY . . . PA 8 32.31 -54.808 -50.219 1 141.7 ? C6 PUY 1120 B 1 
HETATM 25 N N6 PUY . . . PA 8 32.916 -55.728 -49.274 1 130.49 ? N6 PUY 1120 B 1 
HETATM 26 C C9 PUY . . . PA 8 33.621 -55.23 -48.14 1 117.83 ? C9 PUY 1120 B 1 
HETATM 27 C C10 PUY . . . PA 8 32.703 -57.151 -49.31 1 129.55 ? C10 PUY 1120 B 1 
HETATM 28 C C5 PUY . . . PA 8 32.283 -54.01 -51.385 1 155 ? C5 PUY 1120 B 1 
HETATM 29 N N7 PUY . . . PA 8 33.058 -53.678 -52.385 1 150.06 ? N7 PUY 1120 B 1 
HETATM 30 C C8 PUY . . . PA 8 32.452 -52.843 -53.22 1 158.12 ? C8 PUY 1120 B 1 
HETATM 31 C C2' PUY . . . PA 8 28.996 -52.321 -53.054 1 201.78 ? C2' PUY 1120 B 1 
HETATM 32 O O2' PUY . . . PA 8 28.108 -52.44 -54.189 1 234.27 ? O2' PUY 1120 B 1 
HETATM 33 C C3' PUY . . . PA 8 28.23 -51.517 -52.027 1 192.68 ? C3' PUY 1120 B 1 
HETATM 34 N N3' PUY . . . PA 8 26.775 -51.413 -52.094 1 202.81 ? N3' PUY 1120 B 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    47 
_model_server_stats.query_time_ms           278 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           34 
#