SMTL ID : 6az1.1

Cryo-EM structure of the small subunit of Leishmania ribosome bound to paromomycin

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-mer

Ligands

24 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 1 residues within 4Å: Chain C: R.66 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain 7: G.559 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain 7: A.1890 Chain S: E.36 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain 7: A.1548 Chain L: T.145 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain 7: A.783, C.835, C.836 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain 7: G.611, A.629 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain 1: G.18 Chain 7: G.1189, G.2192 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain 7: A.1109, A.1112, C.1209, C.1210 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain 7: G.432, C.452 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain 7: C.470, G.472 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain 7: G.1151 No protein-ligand interaction detected (PLIP) MG.18: 1 residues within 4Å: Chain 7: G.1531 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain 7: C.1237, G.1238 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain 7: G.406 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain 7: G.2163, U.2164 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain 7: G.1139 No protein-ligand interaction detected (PLIP) MG.23: 1 residues within 4Å: Chain 7: G.1995 No protein-ligand interaction detected (PLIP) MG.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.27: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.30: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

6 x PAR: PAROMOMYCIN(Non-functional Binders)(Non-covalent)

PAR.5: 11 residues within 4Å: Chain 7: G.2062, C.2064, G.2065, U.2066, C.2155, A.2156, A.2157, A.2158, A.2159, G.2160, U.2161 No protein-ligand interaction detected (PLIP) PAR.6: 11 residues within 4Å: Chain 7: A.1290, U.1291, U.1292, G.1293, G.1294, G.1295, U.1419, U.1420, C.1421, U.1422, G.1423 No protein-ligand interaction detected (PLIP) PAR.7: 12 residues within 4Å: Chain 7: A.1509, C.1510, C.1511, U.1637, U.1638, G.1639, G.1664, U.1815, G.1818, G.1819, U.2002 Chain L: R.141 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:R.141, L:R.141 PAR.8: 12 residues within 4Å: Chain 7: G.20, A.22, G.23, U.24, A.26, G.646, U.647, A.648, U.649, A.650, U.651 Chain P: G.106 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.106 PAR.9: 10 residues within 4Å: Chain 7: U.2067, G.2068, U.2069, U.2070, A.2149, G.2150, G.2151, A.2152, A.2153, G.2154 No protein-ligand interaction detected (PLIP) PAR.10: 8 residues within 4Å: Chain 7: U.365, G.366, A.367, A.2085, A.2086, C.2132, G.2133, A.2134 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shalev-Benami, M. et al., Atomic resolution snapshot of Leishmania ribosome inhibition by the aminoglycoside paromomycin. Nat Commun (2017)

Release Date

2017-12-06

Peptides

Ribosomal protein s1e: A
ribosomal protein S2: B
ribosomal protein S3: C
ribosomal protein S4: D
ribosomal protein S4e: E
ribosomal protein S5: F
ribosomal protein S6e: G
ribosomal protein S7: H
ribosomal protein S7e: I
ribosomal protein S8: J
ribosomal protein S8e: K
ribosomal protein S9: L
ribosomal protein S10: M
ribosomal protein S10e: N
ribosomal protein S11: O
ribosomal protein S12: P
ribosomal protein S12e: Q
ribosomal protein S13: R
ribosomal protein S14: S
ribosomal protein S15: T
ribosomal protein S17: U
ribosomal protein S17e: V
ribosomal protein S19: W
ribosomal protein S19e: X
ribosomal protein S21e: Y
ribosomal protein S24e: Z
ribosomal protein S25e: 0
ribosomal protein S26e: 1
ribosomal protein S27e: 2
ribosomal protein S28e: 3
ribosomal protein S30e: 4
ribosomal protein S31e: 5
LACK1: 6

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

U
U

V
V

W
W

X
X

Y
Y

Z
Z

0
a

1
b

2
c

3
d

4
e

5
f

6
g

Ribosomal protein s1e

ribosomal protein S2

ribosomal protein S3

ribosomal protein S4

ribosomal protein S4e

ribosomal protein S5

ribosomal protein S6e

ribosomal protein S7

ribosomal protein S7e

ribosomal protein S8

ribosomal protein S8e

ribosomal protein S9

ribosomal protein S10

ribosomal protein S10e

ribosomal protein S11

ribosomal protein S12

ribosomal protein S12e

ribosomal protein S13

ribosomal protein S14

ribosomal protein S15

ribosomal protein S17

ribosomal protein S17e

ribosomal protein S19

ribosomal protein S19e

ribosomal protein S21e

ribosomal protein S24e

ribosomal protein S25e

ribosomal protein S26e

ribosomal protein S27e

ribosomal protein S28e

ribosomal protein S30e

ribosomal protein S31e

LACK1

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