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SMTL ID : 4r17.1

Ligand-induced aziridine-formation at subunit beta5 of the yeast 20S proteasome

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

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

Ligands

11 x MG: MAGNESIUM ION(Non-covalent)

MG.1:	5 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:T.17, G:Y.128, G:R.131, G:M.134, H₂O.28
MG.2:	2 residues within 4Å: Chain H: Q.91 Chain N: D.51 No protein-ligand interaction detected (PLIP)
MG.3:	4 residues within 4Å: Chain I: A.175, D.176, D.178, S.181 6 PLIP interactions: 3 interactions with chain I, 3 Ligand-Water interactions Metal complexes: I:A.175, I:D.178, I:S.181, H₂O.39, H₂O.39, H₂O.44
MG.4:	3 residues within 4Å: Chain I: R.28, A.179, D.205 No protein-ligand interaction detected (PLIP)
MG.5:	3 residues within 4Å: Chain J: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP)
MG.7:	6 residues within 4Å: Chain K: R.19, A.165, D.168, A.169, S.171 Chain W: D.205 5 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W, 1 Ligand-Water interactions Metal complexes: K:A.165, K:D.168, K:S.171, W:D.205, H₂O.49
MG.8:	3 residues within 4Å: Chain K: I.82, N.85, L.86 3 PLIP interactions: 1 interactions with chain K, 2 Ligand-Water interactions Metal complexes: K:I.82, H₂O.50, H₂O.50
MG.9:	5 residues within 4Å: Chain 0: L.47 Chain N: R.19, I.163, D.166, S.169 3 PLIP interactions: 3 interactions with chain N Metal complexes: N:I.163, N:D.166, N:S.169
MG.10:	7 residues within 4Å: Chain L: D.222 Chain V: R.19, G.162, I.163, D.166, L.167, S.169 5 PLIP interactions: 1 interactions with chain L, 3 interactions with chain V, 1 Ligand-Water interactions Metal complexes: L:D.222, V:I.163, V:D.166, V:S.169, H₂O.97
MG.12:	6 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.165, D.168, A.169, S.171 5 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: Y:A.165, Y:D.168, Y:S.171, I:D.205, H₂O.111
MG.13:	4 residues within 4Å: Chain Z: T.192, H.195, I.196, V.198 5 PLIP interactions: 3 interactions with chain Z, 2 Ligand-Water interactions Metal complexes: Z:T.192, Z:H.195, Z:V.198, H₂O.35, H₂O.117

2 x 3K4: (2S,3S)-3-methylaziridine-2-carboxylic acid(Covalent)

3K4.6:	8 residues within 4Å: Chain K: T.2, D.17, K.33, G.130, S.131, G.132, Y.170, S.171 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:S.131, K:G.132, K:Y.170
3K4.11:	8 residues within 4Å: Chain Y: T.2, D.17, K.33, G.130, S.131, G.132, Y.170, S.171 3 PLIP interactions: 3 interactions with chain Y Hydrogen bonds: Y:S.131, Y:G.132, Y:Y.170

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Dubiella, C. et al., Selective inhibition of the immunoproteasome by ligand-induced crosslinking of the active site. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-10-15

Peptides

Proteasome subunit alpha type-2: AO
Proteasome subunit alpha type-3: BP
Proteasome subunit alpha type-4: CQ
Proteasome subunit alpha type-5: DR
Proteasome subunit alpha type-6: ES
Proteasome subunit alpha type-7: FT
Proteasome subunit alpha type-1: GU
Proteasome subunit beta type-2: HV
Proteasome subunit beta type-3: IW
Proteasome subunit beta type-4: JX
Proteasome subunit beta type-5: KY
Proteasome subunit beta type-6: LZ
Proteasome subunit beta type-7: M0
Proteasome subunit beta type-1: 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

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

Proteasome subunit alpha type-2

Toggle Identical (AO)

Proteasome subunit alpha type-3

Toggle Identical (BP)

Proteasome subunit alpha type-4

Toggle Identical (CQ)

Proteasome subunit alpha type-5

Toggle Identical (DR)

Proteasome subunit alpha type-6

Toggle Identical (ES)

Proteasome subunit alpha type-7

Toggle Identical (FT)

Proteasome subunit alpha type-1

Toggle Identical (GU)

Proteasome subunit beta type-2

Toggle Identical (HV)

Proteasome subunit beta type-3

Toggle Identical (IW)

Proteasome subunit beta type-4

Toggle Identical (JX)

Proteasome subunit beta type-5

Toggle Identical (KY)

Proteasome subunit beta type-6

Toggle Identical (LZ)

Proteasome subunit beta type-7

Toggle Identical (M0)

Proteasome subunit beta type-1

Toggle Identical (N1)

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