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SMTL ID : 5jhr.1

Yeast 20S proteasome in complex with the peptidic epoxyketone inhibitor 27

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

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

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1:	5 residues within 4Å: Chain G: T.17, Y.128, R.131, A.132, M.134 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:T.17, G:Y.128, G:R.131, G:M.134
MG.3:	4 residues within 4Å: Chain I: A.175, 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.4:	6 residues within 4Å: Chain I: D.205 Chain Y: A.165, H.166, D.168, A.169, S.171 4 PLIP interactions: 3 interactions with chain Y, 1 interactions with chain I Metal complexes: Y:A.165, Y:D.168, Y:S.171, I:D.205
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 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.9:	7 residues within 4Å: Chain L: D.222 Chain V: G.162, I.163, W.164, D.166, L.167, S.169 4 PLIP interactions: 3 interactions with chain V, 1 interactions with chain L Metal complexes: V:I.163, V:D.166, V:S.169, L:D.222
MG.10:	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:	6 residues within 4Å: Chain Z: R.28, T.192, H.195, I.196, V.198, D.222 3 PLIP interactions: 3 interactions with chain Z Metal complexes: Z:T.192, Z:H.195, Z:V.198

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

CL.2:	3 residues within 4Å: Chain G: R.120, N.123 Chain H: Y.69 Ligand excluded by PLIP
CL.11:	3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP
CL.12:	3 residues within 4Å: Chain U: F.73, C.74, K.98 Ligand excluded by PLIP

2 x 6KF: (2S)-2-azido-N-[(2S)-3-(biphenyl-4-yl)-1-{[(2S)-1-{[(2S,3S,4R)-3,5-dihydroxy-4-methylpentan-2-yl]amino}-1-oxo-3-phenylpropan-2-yl]amino}-1-oxopropan-2-yl]-3-phenylpropanamide (non-preferred name)(Covalent)

6KF.6:

20 residues within 4Å:

Chain K: T.1, R.19, A.20, T.21, A.22, A.27, K.33, G.47, A.49, S.131, Y.170
Chain L: H.108, S.124, F.125, D.126, P.127, V.128, R.137, A.138
Ligands: MES.8

13 PLIP interactions:

6 interactions with chain K, 7 interactions with chain L

Hydrophobic interactions: K:A.27, L:H.108, L:D.126, L:P.127, L:V.128
Hydrogen bonds: K:T.21, K:T.21, K:G.47, K:G.47, K:A.49, L:H.108, L:D.126
pi-Stacking: L:H.108

6KF.13:

19 residues within 4Å:

Chain Y: T.1, R.19, A.20, T.21, A.27, K.33, G.47, A.49, S.131, Y.170
Chain Z: H.108, S.124, F.125, D.126, P.127, V.128, R.137, A.138
Ligands: MES.14

11 PLIP interactions:

6 interactions with chain Y, 5 interactions with chain Z

Hydrophobic interactions: Y:A.27, Z:H.108, Z:D.126, Z:V.128
Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:A.49, Z:D.126
pi-Stacking: Z:H.108

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

MES.8:	11 residues within 4Å: Chain K: T.1, A.46, G.47, S.96, M.97, G.98, Y.114, S.117, G.130, S.131 Ligands: 6KF.6 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:T.1, K:G.47, K:S.131
MES.14:	9 residues within 4Å: Chain Y: T.1, G.47, S.96, M.97, Y.114, S.117, G.130, S.131 Ligands: 6KF.13 3 PLIP interactions: 3 interactions with chain Y Hydrogen bonds: Y:T.1, Y:G.47, Y:S.131

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Xin, B.T. et al., Structure-Based Design of beta 5c Selective Inhibitors of Human Constitutive Proteasomes. J.Med.Chem. (2016)

Release Date

2016-08-03

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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