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SMTL ID : 3nzj.1

Crystal structure of yeast 20S proteasome in complex with ligand 2a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

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

Ligands

2 x BOC- TY5- ALA- TRO- ABN: TMC-95A mimic ligand 2a(Non-covalent)

BOC-TY5-ALA-TRO-ABN.1:

19 residues within 4Å:

Chain K: T.76, R.94, A.95, T.96, A.97, G.98, V.106, K.108, M.120, G.122, G.123, A.124
Chain L: Y.24, P.123, Y.125, H.127, D.145, P.146
Ligands: MES.3

16 PLIP interactions:

6 interactions with chain L, 10 interactions with chain K

Hydrophobic interactions: L:Y.24, L:Y.125, L:H.127, L:P.146, K:V.106, K:M.120, K:A.124
Hydrogen bonds: L:D.145, L:D.145, K:T.76, K:T.96, K:T.96, K:T.96, K:G.98, K:G.122, K:A.124

BOC-TY5-ALA-TRO-ABN.2:

19 residues within 4Å:

Chain Y: T.76, R.94, A.95, T.96, A.97, G.98, V.106, K.108, M.120, G.122, G.123, A.124
Chain Z: Y.24, P.123, Y.125, H.127, D.145, P.146
Ligands: MES.4

16 PLIP interactions:

6 interactions with chain Z, 10 interactions with chain Y

Hydrophobic interactions: Z:Y.24, Z:Y.125, Z:H.127, Z:P.146, Y:V.106, Y:M.120, Y:A.124
Hydrogen bonds: Z:D.145, Z:D.145, Y:T.76, Y:T.96, Y:T.96, Y:T.96, Y:G.98, Y:G.122, Y:A.124

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3:	9 residues within 4Å: Chain K: T.76, T.96, A.121, G.122, G.205, S.206, Y.245 Ligands: BOC-TY5-ALA-TRO-ABN.1, BOC-TY5-ALA-TRO-ABN.1 4 PLIP interactions: 4 interactions with chain K Hydrogen bonds: K:T.76, K:G.122, K:G.122, K:S.206
MES.4:	9 residues within 4Å: Chain Y: T.76, T.96, A.121, G.122, G.205, S.206, Y.245 Ligands: BOC-TY5-ALA-TRO-ABN.2, BOC-TY5-ALA-TRO-ABN.2 4 PLIP interactions: 4 interactions with chain Y Hydrogen bonds: Y:T.76, Y:G.122, Y:G.122, Y:S.206

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Groll, M. et al., 20S proteasome inhibition: designing noncovalent linear peptide mimics of the natural product TMC-95A. Chemmedchem (2010)

Release Date

2011-02-16

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
1

N
N

1
2

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Proteasome component Y7

Toggle Identical (AO)

Proteasome component Y13

Toggle Identical (BP)

Proteasome component PRE6

Toggle Identical (CQ)

Proteasome component PUP2

Toggle Identical (DR)

Proteasome component PRE5

Toggle Identical (ES)

Proteasome component C1

Toggle Identical (FT)

Proteasome component C7-alpha

Toggle Identical (GU)

Proteasome component PUP1

Toggle Identical (HV)

Proteasome component PUP3

Toggle Identical (IW)

Proteasome component C11

Toggle Identical (JX)

Proteasome component PRE2

Toggle Identical (KY)

Proteasome component C5

Toggle Identical (LZ)

Proteasome component PRE4

Toggle Identical (M0)

Proteasome component PRE3

Toggle Identical (N1)

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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

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