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SMTL ID : 4y81.1

Yeast 20S proteasome in complex with Ac-PAY-ep

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

4 x ACE- PRO- ALA- TYE- POL: Ac-PAY-ep(Non-covalent)

ACE-PRO-ALA-TYE-POL.1:	16 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, A.27, V.31, K.33, M.45, G.47, A.49, Q.53, S.131, Y.170 Chain L: D.126, S.130 Ligands: MES.11 13 PLIP interactions: 12 interactions with chain K, 1 interactions with chain L Hydrophobic interactions: K:A.27, K:V.31, K:M.45 Hydrogen bonds: K:T.21, K:T.21, K:G.47, K:G.47, K:G.47, K:A.49, K:Q.53, L:S.130 Water bridges: K:T.21, K:T.21
ACE-PRO-ALA-TYE-POL.2:	16 residues within 4Å: Chain H: H.114, S.118 Chain N: T.1, R.19, T.20, T.21, T.22, T.31, K.33, R.45, S.46, G.47, A.49, T.52, Q.53, S.168 14 PLIP interactions: 14 interactions with chain N Hydrophobic interactions: N:T.20, N:T.22, N:T.31 Hydrogen bonds: N:T.21, N:T.21, N:R.45, N:R.45, N:G.47, N:G.47, N:G.47, N:A.49, N:Q.53 Water bridges: N:A.50, N:S.129
ACE-PRO-ALA-TYE-POL.3:	16 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, A.27, V.31, K.33, M.45, G.47, A.49, Q.53, S.131, Y.170 Chain Z: D.126, S.130 Ligands: MES.17 14 PLIP interactions: 12 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: Y:A.27, Y:V.31, Y:M.45 Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:G.47, Y:A.49, Y:Q.53, Z:S.130, Z:S.130 Water bridges: Y:T.21, Y:T.21
ACE-PRO-ALA-TYE-POL.4:	16 residues within 4Å: Chain 1: T.1, R.19, T.20, T.21, T.22, T.31, K.33, R.45, S.46, G.47, A.49, T.52, Q.53, S.168 Chain V: H.114, S.118 13 PLIP interactions: 1 interactions with chain V, 12 interactions with chain 1 Water bridges: V:S.118 Hydrophobic interactions: 1:T.20, 1:T.22, 1:T.31 Hydrogen bonds: 1:T.21, 1:T.21, 1:R.45, 1:R.45, 1:G.47, 1:G.47, 1:G.47, 1:A.49, 1:Q.53

9 x MG: MAGNESIUM ION(Non-covalent)

MG.5:	6 residues within 4Å: Chain C: Q.117, Y.120, T.121, P.128, F.129, P.152 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:Q.117
MG.6:	5 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:T.17, G:R.131, G:M.134
MG.8:	5 residues within 4Å: Chain I: A.175, D.176, D.178, S.181, D.205 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:A.175, I:D.178, I:S.181
MG.9:	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.20
MG.10:	6 residues within 4Å: Chain K: A.165, H.166, D.168, A.169, S.171 Chain W: D.205 4 PLIP interactions: 3 interactions with chain K, 1 interactions with chain W Metal complexes: K:A.165, K:D.168, K:S.171, W:D.205
MG.12:	8 residues within 4Å: Chain L: D.222 Chain V: G.162, I.163, W.164, N.165, D.166, L.167, S.169 3 PLIP interactions: 2 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.163, V:D.166, L:D.222
MG.13:	5 residues within 4Å: Chain 0: L.47 Chain N: R.19, I.163, D.166, S.169 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:I.163, N:S.169
MG.15:	3 residues within 4Å: Chain X: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP)
MG.16:	5 residues within 4Å: Chain Z: R.28, T.192, H.195, V.198, D.222 2 PLIP interactions: 2 interactions with chain Z Metal complexes: Z:T.192, Z:V.198

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7:	3 residues within 4Å: Chain G: R.120, N.123 Chain H: Y.69 Ligand excluded by PLIP
CL.14:	3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP

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

MES.11:	10 residues within 4Å: Chain K: T.1, G.47, S.96, M.97, G.98, S.117, G.130, S.131 Ligands: ACE-PRO-ALA-TYE-POL.1, ACE-PRO-ALA-TYE-POL.1 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:S.131
MES.17:	10 residues within 4Å: Chain Y: T.1, G.47, S.96, M.97, G.98, S.117, G.130, S.131 Ligands: ACE-PRO-ALA-TYE-POL.3, ACE-PRO-ALA-TYE-POL.3 1 PLIP interactions: 1 interactions with chain Y Hydrogen bonds: Y:S.131

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Huber, E.M. et al., Systematic Analyses of Substrate Preferences of 20S Proteasomes Using Peptidic Epoxyketone Inhibitors. J.Am.Chem.Soc. (2015)

Release Date

2015-06-17

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
Probable 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)

Probable 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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