SMTL ID : 6okk.1

Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine, small subunit

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.30 Å

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-mer

Ligands

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

MG.1: 2 residues within 4Å: Chain A: G.10, A.1930 No protein-ligand interaction detected (PLIP) MG.2: 2 residues within 4Å: Chain A: G.16, C.621 No protein-ligand interaction detected (PLIP) MG.3: 2 residues within 4Å: Chain A: A.102, C.367 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: A.102, U.103, U.104, A.366, C.367 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain A: C.49, A.431 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: A.452, U.454, A.464 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain A: A.60, A.62, A.459 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: A.87 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain A: G.97 No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain A: G.390 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: A.393, U.408 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain A: G.328, G.343, A.347 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain A: G.42, A.43, U.100 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain A: A.43, U.44, A.47 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain A: C.430, C.433, A.434, G.435 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain A: G.369, G.383, A.384, U.385 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain A: A.407, U.408 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain A: A.55, C.430, G.432 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain A: G.465, A.466, G.467 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain A: A.28 No protein-ligand interaction detected (PLIP) MG.21: 4 residues within 4Å: Chain A: U.35, G.522, C.537, U.538 No protein-ligand interaction detected (PLIP) MG.22: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 2 residues within 4Å: Chain A: G.568, G.569 No protein-ligand interaction detected (PLIP) MG.24: 2 residues within 4Å: Chain A: A.577, G.578 No protein-ligand interaction detected (PLIP) MG.25: 2 residues within 4Å: Chain A: A.611, A.612 No protein-ligand interaction detected (PLIP) MG.26: 4 residues within 4Å: Chain A: G.377, A.612, A.614, G.620 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain A: C.621, U.1200, G.1201 No protein-ligand interaction detected (PLIP) MG.28: 4 residues within 4Å: Chain A: U.625, A.626, A.627, A.628 No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Chain A: C.630 No protein-ligand interaction detected (PLIP) MG.30: 5 residues within 4Å: Chain A: A.629, C.630, G.631, C.632, U.1100 No protein-ligand interaction detected (PLIP) MG.31: 3 residues within 4Å: Chain A: A.637, G.638, C.1038 No protein-ligand interaction detected (PLIP) MG.32: 3 residues within 4Å: Chain A: A.642, A.643, A.869 No protein-ligand interaction detected (PLIP) MG.33: 3 residues within 4Å: Chain A: A.930, A.931, G.934 No protein-ligand interaction detected (PLIP) MG.34: 2 residues within 4Å: Chain A: G.1104, A.1105 No protein-ligand interaction detected (PLIP) MG.35: 3 residues within 4Å: Chain 2: N.14 Chain A: C.1006, G.1007 No protein-ligand interaction detected (PLIP) MG.36: 3 residues within 4Å: Chain A: U.1059, G.1060, G.1080 No protein-ligand interaction detected (PLIP) MG.37: 2 residues within 4Å: Chain A: U.1059, U.1081 No protein-ligand interaction detected (PLIP) MG.38: 2 residues within 4Å: Chain A: G.1054, G.1055 No protein-ligand interaction detected (PLIP) MG.39: 5 residues within 4Å: Chain A: G.964, U.965, G.983, A.984, U.986 No protein-ligand interaction detected (PLIP) MG.40: 2 residues within 4Å: Chain A: G.997, A.998 No protein-ligand interaction detected (PLIP) MG.41: 1 residues within 4Å: Chain A: G.945 No protein-ligand interaction detected (PLIP) MG.42: 3 residues within 4Å: Chain 2: G.16 Chain A: A.1010, G.1011 No protein-ligand interaction detected (PLIP) MG.43: 2 residues within 4Å: Chain A: A.1047, A.1048 No protein-ligand interaction detected (PLIP) MG.44: 4 residues within 4Å: Chain A: C.634, A.1036, U.1037 Chain U: M.4 No protein-ligand interaction detected (PLIP) MG.45: 1 residues within 4Å: Chain A: A.1094 No protein-ligand interaction detected (PLIP) MG.46: 3 residues within 4Å: Chain A: G.1209, G.1210, G.1211 No protein-ligand interaction detected (PLIP) MG.47: 4 residues within 4Å: Chain A: C.1260, A.1261, G.1876 Chain M: Y.143 No protein-ligand interaction detected (PLIP) MG.48: 4 residues within 4Å: Chain A: G.1926, U.1927, G.2085, A.2086 No protein-ligand interaction detected (PLIP) MG.49: 6 residues within 4Å: Chain A: A.2055, C.2056, G.2059, G.2060, U.2062, U.2063 No protein-ligand interaction detected (PLIP) MG.50: 2 residues within 4Å: Chain A: A.2058, U.2062 No protein-ligand interaction detected (PLIP) MG.51: 5 residues within 4Å: Chain A: U.2053, A.2054, A.2055, G.2059, G.2060 No protein-ligand interaction detected (PLIP) MG.52: 3 residues within 4Å: Chain A: G.20, U.21, A.612 No protein-ligand interaction detected (PLIP) MG.53: 1 residues within 4Å: Chain A: G.521 No protein-ligand interaction detected (PLIP) MG.54: 2 residues within 4Å: Chain A: U.1405, G.1406 No protein-ligand interaction detected (PLIP) MG.55: 2 residues within 4Å: Chain A: A.169, C.170 No protein-ligand interaction detected (PLIP) MG.56: 3 residues within 4Å: Chain A: G.394, U.408, G.429 No protein-ligand interaction detected (PLIP) MG.57: 5 residues within 4Å: Chain A: G.559, G.560, C.561, A.562, A.563 No protein-ligand interaction detected (PLIP) MG.58: 5 residues within 4Å: Chain A: A.1062, G.1063, A.1074, C.2076 Ligands: MG.59 No protein-ligand interaction detected (PLIP) MG.59: 4 residues within 4Å: Chain A: G.1063, U.1073, A.1074 Ligands: MG.58 No protein-ligand interaction detected (PLIP) MG.60: 4 residues within 4Å: Chain A: A.1048, G.1049, A.1083, U.1084 No protein-ligand interaction detected (PLIP) MG.61: 3 residues within 4Å: Chain A: A.1431, G.1432, A.1433 No protein-ligand interaction detected (PLIP) MG.62: 3 residues within 4Å: Chain A: G.1430, A.1431, G.1432 No protein-ligand interaction detected (PLIP) MG.63: 4 residues within 4Å: Chain A: G.1374, C.1375, G.1674, G.1675 No protein-ligand interaction detected (PLIP) MG.64: 4 residues within 4Å: Chain A: A.1305, C.1306, U.1307, G.1701 No protein-ligand interaction detected (PLIP) MG.65: 3 residues within 4Å: Chain A: A.1303, A.1304, C.1896 No protein-ligand interaction detected (PLIP) MG.66: 2 residues within 4Å: Chain A: C.1278, U.1703 No protein-ligand interaction detected (PLIP) MG.67: 4 residues within 4Å: Chain A: A.1297, G.1302, A.1897, A.1899 No protein-ligand interaction detected (PLIP)

1 x 34G: emetine(Non-covalent)

34G.68: 8 residues within 4Å: Chain A: G.973, U.1068, C.1069, C.1075, C.1076, G.2060, U.2061 Chain P: L.151 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.69: 5 residues within 4Å: Chain T: C.19, C.22, N.24, C.37, C.40 4 PLIP interactions: 4 interactions with chain T Metal complexes: T:C.19, T:C.22, T:C.37, T:C.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wong, W. et al., Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine. Elife (2014)

Release Date

2019-05-22

Peptides

40S ribosomal protein S3a: B
40S ribosomal protein SA: C
40S ribosomal protein S3: D
40S ribosomal protein S9: E
40S ribosomal protein S4: F
40S ribosomal protein S5: G
40S ribosomal protein S6: H
40S ribosomal protein S5: I
40S ribosomal protein S7: J
40S ribosomal protein S15A: K
40S ribosomal protein S8: L
40S ribosomal protein S16: M
40S ribosomal protein S20e: N
40S ribosomal protein S10: O
40S ribosomal protein S11: P
40S ribosomal protein S23: Q
40S ribosomal protein S12: R
40S ribosomal protein S18: S
40S ribosomal protein S29: T
40S ribosomal protein S15: U
40S ribosomal protein S11: V
40S ribosomal protein S17: W
40S ribosomal protein S19: X
40S ribosomal protein S19: Y
40S ribosomal protein S21: Z
40S ribosomal protein S24: 0
40S ribosomal protein S25: 1
40S ribosomal protein S26: 2
40S ribosomal protein S27: 3
40S ribosomal protein S28e: 4
40S ribosomal protein S30: 5

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

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

40S ribosomal protein S3a

40S ribosomal protein SA

40S ribosomal protein S3

40S ribosomal protein S9

40S ribosomal protein S4

40S ribosomal protein S5

40S ribosomal protein S6

40S ribosomal protein S5

40S ribosomal protein S7

40S ribosomal protein S15A

40S ribosomal protein S8

40S ribosomal protein S16

40S ribosomal protein S20e

40S ribosomal protein S10

40S ribosomal protein S11

40S ribosomal protein S23

40S ribosomal protein S12

40S ribosomal protein S18

40S ribosomal protein S29

40S ribosomal protein S15

40S ribosomal protein S11

40S ribosomal protein S17

40S ribosomal protein S19

40S ribosomal protein S19

40S ribosomal protein S21

40S ribosomal protein S24

40S ribosomal protein S25

40S ribosomal protein S26

40S ribosomal protein S27

40S ribosomal protein S28e

40S ribosomal protein S30

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