SMTL ID : 2hhh.1

Crystal structure of kasugamycin bound to the 30S ribosomal subunit

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.35 Å

Oligo State

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

Ligands

2 x KSG: (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2-AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6-TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE(Non-functional Binders)(Non-covalent)

KSG.1: 9 residues within 4Å: Chain A: A.776, A.778, C.779, G.904, U.1476, A.1477, G.1482, G.1483, U.1484 No protein-ligand interaction detected (PLIP) KSG.2: 5 residues within 4Å: Chain A: G.677, U.772, U.773 Chain G: G.81, G.82 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schluenzen, F. et al., The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation. Nat.Struct.Mol.Biol. (2006)

Release Date

2006-09-26

Peptides

30S ribosomal protein S2: B
30S ribosomal protein S3: C
30S ribosomal protein S4: D
30S ribosomal protein S5: E
30S ribosomal protein S6: F
30S ribosomal protein S7: G
30S ribosomal protein S8: H
30S ribosomal protein S9: I
30S ribosomal protein S10: J
30S ribosomal protein S11: K
30S ribosomal protein S12: L
30S ribosomal protein S13: M
30S ribosomal protein S14: N
30S ribosomal protein S15: O
30S ribosomal protein S16: P
30S ribosomal protein S17: Q
30S ribosomal protein S18: R
30S ribosomal protein S19: S
30S ribosomal protein S20: T
30S ribosomal protein Thx: U

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

30S ribosomal protein S2

30S ribosomal protein S3

30S ribosomal protein S4

30S ribosomal protein S5

30S ribosomal protein S6

30S ribosomal protein S7

30S ribosomal protein S8

30S ribosomal protein S9

30S ribosomal protein S10

30S ribosomal protein S11

30S ribosomal protein S12

30S ribosomal protein S13

30S ribosomal protein S14

30S ribosomal protein S15

30S ribosomal protein S16

30S ribosomal protein S17

30S ribosomal protein S18

30S ribosomal protein S19

30S ribosomal protein S20

30S ribosomal protein Thx

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