SMTL ID : 8fvy.1

40S subunit of the Giardia lamblia 80S ribosome

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-mer

Ligands

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

MG.1: 3 residues within 4Å: Chain A: G.499, A.500, A.501 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: G.16, A.500 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: C.116, C.117, G.160 No protein-ligand interaction detected (PLIP) MG.4: 1 residues within 4Å: Chain A: U.157 No protein-ligand interaction detected (PLIP) MG.5: 5 residues within 4Å: Chain A: A.87, G.88, G.89, G.272, C.273 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: C.294 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: A.80, G.82, G.315 Chain F: R.3 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain A: G.312, A.313 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain A: A.299, C.314 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain A: G.335, C.336 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: C.503, U.782 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Chain 0: G.16 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Chain N: K.9 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain A: G.730 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain A: A.718, U.719 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain A: C.494, C.837, C.840, G.841 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: G.499, G.781 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain A: G.850, G.851 No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain A: U.1413, A.1414, A.1415, G.1419, G.1420 No protein-ligand interaction detected (PLIP) MG.20: 5 residues within 4Å: Chain A: A.1415, G.1419, G.1420, A.1422, U.1423 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain A: U.1421, A.1422 No protein-ligand interaction detected (PLIP) MG.22: 3 residues within 4Å: Chain A: C.1416, A.1422, U.1423 No protein-ligand interaction detected (PLIP) MG.23: 3 residues within 4Å: Chain A: G.1314, U.1315, G.1445 No protein-ligand interaction detected (PLIP)

1 x YAT: emetine(Non-covalent)

YAT.24: 11 residues within 4Å: Chain A: G.655, A.749, U.750, C.751, C.757, C.758, G.1420, U.1421 Chain G: G.117, G.118 Chain O: L.145 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:L.145

1 x ZN: ZINC ION(Non-covalent)

ZN.25: 6 residues within 4Å: Chain 0: C.23, Q.24, N.25, C.26, Y.73, C.77 1 PLIP interactions: 1 interactions with chain 0 Metal complexes: 0:C.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eiler, D.R. et al., The Giardia lamblia ribosome structure reveals divergence in several biological pathways and the mode of emetine function. Structure (2024)

Release Date

2024-01-24

Peptides

40S ribosomal protein SA: B
40S ribosomal protein S3a: C
Ribosomal protein S2: D
Ribosomal protein S3: E
40S ribosomal protein S4: F
SSU ribosomal protein S7P (Fragment): G
40S ribosomal protein S6: H
40S ribosomal protein S7: I
40S ribosomal protein S8: J
Ribosomal protein S9: K
Ribosomal protein S10B: L
SSU ribosomal protein S17P: M
Ribosomal protein S13: N
Ribosomal protein S14: O
Ribosomal protein S15: P
Ribosomal protein S16: Q
Ribosomal protein S17: R
Ribosomal protein S18: S
SSU ribosomal protein S19E (Fragment): T
Ribosomal protein S20: U
40S ribosomal protein S21: V
SSU ribosomal protein S8P (Fragment): W
SSU ribosomal protein S12P: X
Ribosomal protein S24: Y
40S ribosomal protein S25: Z
40S ribosomal protein S26: 0
Ribosomal protein S27: 1
Ribosomal protein S28: 2
Ribosomal protein S29A: 3
Ribosomal protein S27a: 4
Ribosomal protein S12: 6
40S ribosomal protein S30: 7

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

C
B

D
C

E
D

F
E

G
F

H
G

I
H

J
I

K
J

L
K

M
L

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
f

6
M

7
e

40S ribosomal protein SA

40S ribosomal protein S3a

Ribosomal protein S2

Ribosomal protein S3

40S ribosomal protein S4

SSU ribosomal protein S7P (Fragment)

40S ribosomal protein S6

40S ribosomal protein S7

40S ribosomal protein S8

Ribosomal protein S9

Ribosomal protein S10B

SSU ribosomal protein S17P

Ribosomal protein S13

Ribosomal protein S14

Ribosomal protein S15

Ribosomal protein S16

Ribosomal protein S17

Ribosomal protein S18

SSU ribosomal protein S19E (Fragment)

Ribosomal protein S20

40S ribosomal protein S21

SSU ribosomal protein S8P (Fragment)

SSU ribosomal protein S12P

Ribosomal protein S24

40S ribosomal protein S25

40S ribosomal protein S26

Ribosomal protein S27

Ribosomal protein S28

Ribosomal protein S29A

Ribosomal protein S27a

Ribosomal protein S12

40S ribosomal protein S30

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