SMTL ID : 6az3.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

PAR.1: 16 residues within 4Å: Chain P: R.65, R.148, G.151, R.156 Chain g: U.769, G.770, G.771, U.772, C.802, A.803, A.804, C.808, U.831, U.832, G.833, A.835 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:R.65, P:R.148, P:R.156 PAR.2: 13 residues within 4Å: Chain C: R.106 Chain L: K.5 Chain M: R.203 Chain g: C.693, A.694, A.695, A.696, C.697, A.698, G.699, C.841, C.842, U.843 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain L Hydrogen bonds: C:R.106, C:R.106, L:K.5 PAR.3: 11 residues within 4Å: Chain P: S.8, K.9, S.11 Chain g: G.1020, G.1021, U.1022, G.1023, G.1161, C.1162, A.1163, C.1164 2 PLIP interactions: 2 interactions with chain P Hydrogen bonds: P:S.8, P:S.11 PAR.4: 10 residues within 4Å: Chain 6: G.104 Chain g: A.468, G.469, U.470, A.471, C.472, G.654, G.655, G.656, G.657 1 PLIP interactions: 1 interactions with chain 6 Hydrogen bonds: 6:G.104 PAR.5: 8 residues within 4Å: Chain g: C.890, G.891, G.892, G.893, G.894, C.898, C.899 Chain i: C.112 No protein-ligand interaction detected (PLIP) PAR.28: 13 residues within 4Å: Ligands: PAR.29 Chain h: G.405, C.409, C.410, A.412, G.413, G.415, U.671, A.1021, U.1022, C.1023, U.1024, G.1025 No protein-ligand interaction detected (PLIP) PAR.29: 15 residues within 4Å: Ligands: PAR.28 Chain h: A.403, U.404, G.405, C.406, U.417, G.418, U.419, U.421, A.422, C.762, G.763, A.764, U.1022, C.1023 No protein-ligand interaction detected (PLIP) PAR.30: 6 residues within 4Å: Chain h: G.446, C.480, G.663, C.667, U.1031, G.1032 No protein-ligand interaction detected (PLIP) PAR.31: 8 residues within 4Å: Chain h: G.518, U.519, A.520, G.550, C.551, G.552, U.555, G.556 No protein-ligand interaction detected (PLIP) PAR.42: 15 residues within 4Å: Chain g: U.437, A.446, A.447, G.448, U.1484, U.1485, G.1501, U.1503 Chain j: G.9 Chain m: C.8, G.9, C.10, G.11, A.12, U.13 No protein-ligand interaction detected (PLIP)

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

MG.6: 3 residues within 4Å: Chain C: G.95 Chain g: G.383, G.385 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain h: U.656 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain g: A.1456, G.1457 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain g: G.18, G.52 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain g: A.690, G.1517, U.1518, G.1519 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain g: U.912, A.942 No protein-ligand interaction detected (PLIP) MG.13: 2 residues within 4Å: Chain g: A.58, U.358 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain g: A.48 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain g: U.1598, C.1619 No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain g: A.59, U.358 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain g: G.1610, C.1611, A.1612 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain g: U.1582, G.1583 Chain h: U.53 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain g: U.305, A.306, G.307 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain g: U.740, C.742 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain g: U.673, G.674 No protein-ligand interaction detected (PLIP) MG.22: 1 residues within 4Å: Chain g: G.247 No protein-ligand interaction detected (PLIP) MG.23: 4 residues within 4Å: Chain C: M.56 Chain g: C.979, C.980, A.982 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Chain g: A.97 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Chain g: G.1212 No protein-ligand interaction detected (PLIP) MG.26: 2 residues within 4Å: Chain g: G.112, U.146 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain g: G.965, G.973 Chain h: G.1395 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Chain h: G.379 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain h: U.662, G.1033, A.1036 No protein-ligand interaction detected (PLIP) MG.34: 3 residues within 4Å: Chain h: C.1192, U.1193, G.1231 No protein-ligand interaction detected (PLIP) MG.35: 1 residues within 4Å: Chain h: A.1225 No protein-ligand interaction detected (PLIP) MG.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain h: C.31, G.33 No protein-ligand interaction detected (PLIP) MG.38: 1 residues within 4Å: Chain h: C.578 No protein-ligand interaction detected (PLIP) MG.39: 1 residues within 4Å: Chain i: A.32 No protein-ligand interaction detected (PLIP) MG.40: 1 residues within 4Å: Chain j: G.36 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain k: A.14 No protein-ligand interaction detected (PLIP) MG.43: 3 residues within 4Å: Chain m: A.104, C.105, A.108 No protein-ligand interaction detected (PLIP) MG.44: 4 residues within 4Å: Chain g: A.380, G.406 Chain m: G.18, A.19 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 uL2: A
ribosomal protein uL3: B
Ribosomal protein L1a, putative: C
60S ribosomal protein L11 (L5, L16): D
60S ribosomal protein L9, putative: E
ribosomal protein eL6: F
60S ribosomal protein L7a: G
ribosomal protein uL13: H
ribosomal protein eL13: I
60S ribosomal protein L23, putative: J
Probable 60S ribosomal protein L14: K
60S ribosomal protein L27A/L29, putative: L
Ribosomal protein L15: M
60S ribosomal protein L10, putative: N
60S ribosomal protein L5, putative: O
60S ribosomal protein L18, putative: P
Ribosomal protein L19e family protein: Q
60S ribosomal protein L18a: R
60S ribosomal protein L21, putative: S
60S ribosomal protein L17, putative: T
60S ribosomal protein L22, putative: U
60S ribosomal protein L23a, putative: V
ribosomal protein uL24: W
ribosomal protein eL24: X
Ribosomal L27e family protein: Y
60S ribosomal protein L28, putative: Z
60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340: 0
60S ribosomal protein L29: 1
60S ribosomal protein L7 family protein: 2
60S ribosomal protein L30: 3
60S ribosomal subunit protein L31, putative: 4
60S_ribosomal_protein_L32/GeneDB:LmjF.21.1720: 5
Ribosomal protein L35Ae family protein: 6
60S ribosomal protein L34, putative: 7
60S ribosomal protein L36, putative: 8
60S ribosomal protein L37: 9
Ribosomal L38e family protein: a
60S ribosomal protein L39, putative: b
Ubiquitin-60S ribosomal protein L40: c
ribosomal protein eL41: d
60S ribosomal protein L37a: e
60S ribosomal protein L44, putative: f

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

7
h

8
i

9
j

a
k

b
l

c
m

d
n

e
o

f
p

ribosomal protein uL2

ribosomal protein uL3

Ribosomal protein L1a, putative

60S ribosomal protein L11 (L5, L16)

60S ribosomal protein L9, putative

ribosomal protein eL6

60S ribosomal protein L7a

ribosomal protein uL13

ribosomal protein eL13

60S ribosomal protein L23, putative

Probable 60S ribosomal protein L14

60S ribosomal protein L27A/L29, putative

Ribosomal protein L15

60S ribosomal protein L10, putative

60S ribosomal protein L5, putative

60S ribosomal protein L18, putative

Ribosomal protein L19e family protein

60S ribosomal protein L18a

60S ribosomal protein L21, putative

60S ribosomal protein L17, putative

60S ribosomal protein L22, putative

60S ribosomal protein L23a, putative

ribosomal protein uL24

ribosomal protein eL24

Ribosomal L27e family protein

60S ribosomal protein L28, putative

60S_ribosomal_protein_L35_putative/GeneDB:LmjF.26.2330/GeneDB:LmjF.26.2340

60S ribosomal protein L29

60S ribosomal protein L7 family protein

60S ribosomal protein L30

60S ribosomal subunit protein L31, putative

60S_ribosomal_protein_L32/GeneDB:LmjF.21.1720

Ribosomal protein L35Ae family protein

60S ribosomal protein L34, putative

60S ribosomal protein L36, putative

60S ribosomal protein L37

Ribosomal L38e family protein

60S ribosomal protein L39, putative

Ubiquitin-60S ribosomal protein L40

ribosomal protein eL41

60S ribosomal protein L37a

60S ribosomal protein L44, putative

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