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SMTL ID : 4qlq.1

yCP in complex with tripeptidic epoxyketone inhibitor 8

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

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.2:	3 residues within 4Å: Chain H: Q.91 Chain N: D.51, N.92 No protein-ligand interaction detected (PLIP)
MG.5:	4 residues within 4Å: Chain I: A.175, D.176, D.178, S.181 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:A.175, I:D.178, I:S.181
MG.6:	6 residues within 4Å: Chain K: R.19, A.165, D.168, A.169, S.171 Chain W: D.205 4 PLIP interactions: 1 interactions with chain W, 3 interactions with chain K Metal complexes: W:D.205, K:A.165, K:D.168, K:S.171
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 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.13:	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.26
MG.16:	5 residues within 4Å: Chain Z: R.28, T.192, H.195, I.196, V.198 3 PLIP interactions: 3 interactions with chain Z Metal complexes: Z:T.192, Z:H.195, Z:V.198

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

MES.3:	6 residues within 4Å: Chain H: A.46, G.47, G.128, S.129 Chain Z: Y.33 Ligands: 38N.4 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:G.47, H:S.129
MES.7:	10 residues within 4Å: Chain K: T.1, G.47, S.96, M.97, G.98, Y.114, S.117, G.130, S.131 Ligands: 38N.8 3 PLIP interactions: 3 interactions with chain K Hydrogen bonds: K:T.1, K:G.47, K:S.131
MES.11:	6 residues within 4Å: Chain L: Y.33 Chain V: A.46, G.47, G.128, S.129 Ligands: 38N.12 2 PLIP interactions: 2 interactions with chain V Hydrogen bonds: V:G.47, V:S.129
MES.14:	10 residues within 4Å: Chain Y: T.1, G.47, S.96, M.97, G.98, D.116, S.117, G.130, S.131 Ligands: 38N.15 3 PLIP interactions: 3 interactions with chain Y Hydrogen bonds: Y:T.1, Y:G.47, Y:S.131

4 x 38N: N-(morpholin-4-ylacetyl)-L-alanyl-N-[(2S,4R)-1-cyclohexyl-5-hydroxy-4-methyl-3-oxopentan-2-yl]-O-methyl-L-tyrosinamide(Covalent)

38N.4:	17 residues within 4Å: Chain H: T.1, R.19, S.20, T.21, Q.22, C.31, K.33, G.45, A.46, G.47, T.48, A.49, T.52, G.168 Chain I: D.125, L.126 Ligands: MES.3 11 PLIP interactions: 8 interactions with chain H, 3 interactions with chain I Hydrogen bonds: H:T.1, H:T.21, H:T.21, H:Q.22, H:G.47, H:G.47, H:A.49, I:D.125, I:D.125 Water bridges: H:A.50 Salt bridges: I:D.125
38N.8:	17 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, V.31, K.32, K.33, M.45, A.46, G.47, G.48, A.49, S.96, Y.170 Chain L: D.126, V.128 Ligands: MES.7 14 PLIP interactions: 12 interactions with chain K, 2 interactions with chain L Hydrophobic interactions: K:T.21, K:V.31, K:M.45, K:A.49 Hydrogen bonds: K:T.21, K:T.21, K:G.47, K:G.47, K:A.49, L:D.126 Water bridges: K:T.21, K:T.21, K:A.50 Salt bridges: L:D.126
38N.12:	17 residues within 4Å: Chain V: T.1, R.19, S.20, T.21, Q.22, C.31, K.33, G.45, A.46, G.47, T.48, A.49, T.52, G.168 Chain W: D.125, L.126 Ligands: MES.11 11 PLIP interactions: 8 interactions with chain V, 3 interactions with chain W Hydrogen bonds: V:T.1, V:T.21, V:T.21, V:Q.22, V:G.47, V:G.47, V:A.49, W:D.125, W:D.125 Water bridges: V:A.50 Salt bridges: W:D.125
38N.15:	17 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, V.31, K.32, K.33, M.45, A.46, G.47, G.48, A.49, S.96, Y.170 Chain Z: D.126, V.128 Ligands: MES.14 14 PLIP interactions: 2 interactions with chain Z, 12 interactions with chain Y Hydrogen bonds: Z:D.126, Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:A.49 Salt bridges: Z:D.126 Hydrophobic interactions: Y:T.21, Y:V.31, Y:M.45, Y:A.49 Water bridges: Y:T.21, Y:T.21, Y:A.50

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

De Bruin, G. et al., Structure-based design of beta 1i or beta 5i specific inhibitors of human immunoproteasomes. J.Med.Chem. (2014)

Release Date

2014-07-23

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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