SMTL ID : 4hrc.1

Crystal structure of yeast 20S proteasome in complex with epoxyketone carmaphycin analogue 3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

6 x OV2: N-hexanoyl-L-valyl-N~1~-[(2R,3S,4S)-1,3-dihydroxy-2,6-dimethylheptan-4-yl]-N~5~,N~5~-dimethyl-L-glutamamide(Covalent)

OV2.1: 16 residues within 4Å: Chain H: T.1, R.19, S.20, T.21, Q.22, K.33, G.45, A.46, G.47, T.48, A.49, T.52, S.129, G.168 Chain I: R.98, D.124 12 PLIP interactions: 9 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:T.21, H:T.21, H:T.21, H:G.47, H:G.47, H:G.47, H:A.49, I:D.124, I:D.124 Water bridges: H:A.50, H:S.129 Hydrophobic interactions: I:D.124 OV2.2: 13 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, A.27, K.33, M.45, G.47, A.49, S.131, Y.170 Chain L: D.126, P.127 12 PLIP interactions: 9 interactions with chain K, 3 interactions with chain L Hydrophobic interactions: K:A.27, L:P.127, L:P.127 Hydrogen bonds: K:T.21, K:T.21, K:G.47, K:G.47, K:A.49, K:S.96, L:D.126 Water bridges: K:S.131, K:S.131 OV2.3: 15 residues within 4Å: Chain H: H.114, S.118 Chain N: T.1, R.19, T.20, T.21, K.33, R.45, S.46, G.47, S.48, A.49, T.94, S.129, S.168 11 PLIP interactions: 11 interactions with chain N Hydrophobic interactions: N:T.20, N:R.45, N:A.49 Hydrogen bonds: N:T.21, N:T.21, N:G.47, N:G.47, N:G.47, N:A.49 Water bridges: N:S.129, N:S.129 OV2.4: 16 residues within 4Å: Chain V: T.1, R.19, S.20, T.21, Q.22, C.31, K.33, A.46, G.47, T.48, A.49, S.129, G.168 Chain W: D.124, L.125, I.126 14 PLIP interactions: 9 interactions with chain V, 5 interactions with chain W Hydrophobic interactions: V:Q.22, V:K.33, W:D.124, W:L.125, W:I.126 Hydrogen bonds: V:T.21, V:T.21, V:G.47, V:G.47, V:A.49, V:S.129, W:D.124, W:D.124 Water bridges: V:S.129 OV2.5: 13 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, A.27, K.33, M.45, G.47, A.49, S.131, Y.170 Chain Z: D.126, P.127 13 PLIP interactions: 11 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: Y:A.27, Y:K.33, Y:K.33, Y:M.45, Z:P.127 Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:G.47, Y:A.49, Z:D.126 Water bridges: Y:S.131 OV2.6: 16 residues within 4Å: Chain 1: T.1, R.19, T.20, T.21, T.22, K.33, R.45, G.47, S.48, A.49, T.94, S.129, S.168 Chain V: H.114, H.116, S.118 8 PLIP interactions: 8 interactions with chain 1 Hydrophobic interactions: 1:T.20, 1:T.22 Hydrogen bonds: 1:T.21, 1:T.21, 1:T.21, 1:G.47, 1:G.47, 1:A.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Trivella, D.B. et al., Enzyme inhibition by hydroamination: design and mechanism of a hybrid carmaphycin-syringolin enone proteasome inhibitor. Chem.Biol. (2014)

Release Date

2014-01-29

Peptides

Proteasome component Y7: AO
Proteasome component Y13: BP
Proteasome component PRE6: CQ
Proteasome component PUP2: DR
Proteasome component PRE5: ES
Proteasome component C1: FT
Proteasome component C7-alpha: GU
Proteasome component PUP1: HV
Proteasome component PUP3: IW
Proteasome component C11: JX
Proteasome component PRE2: KY
Proteasome component C5: LZ
Proteasome component PRE4: M0
Proteasome component PRE3: N1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O
O

B
B

P
P

C
C

Q
Q

D
D

R
R

E
E

S
S

F
F

T
T

G
G

U
U

H
H

V
V

I
I

W
W

J
J

X
X

K
K

Y
Y

L
L

Z
Z

M
M

0
a

N
N

1
b

Proteasome component Y7

Proteasome component Y13

Proteasome component PRE6

Proteasome component PUP2

Proteasome component PRE5

Proteasome component C1

Proteasome component C7-alpha

Proteasome component PUP1

Proteasome component PUP3

Proteasome component C11

Proteasome component PRE2

Proteasome component C5

Proteasome component PRE4

Proteasome component PRE3

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