4no9.1 | SWISS-MODEL Template Library

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SMTL ID : 4no9.1

yCP in complex with Z-Leu-Leu-Leu-epoxyketone

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:	3 residues within 4Å: Chain H: Q.91 Chain N: D.51, N.92 No protein-ligand interaction detected (PLIP)
MG.4:	5 residues within 4Å: Chain I: A.175, D.178, A.179, S.181, D.205 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.178, I:S.181
MG.6:	7 residues within 4Å: Chain K: R.19, A.165, H.166, 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.7:	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.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.11:	7 residues within 4Å: Chain I: D.205 Chain Y: R.19, A.165, H.166, D.168, A.169, S.171 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain Y Metal complexes: I:D.205, Y:A.165, Y:D.168, Y:S.171
MG.12:	4 residues within 4Å: Chain Z: T.192, H.195, 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 2L0: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2R,3S,4S)-1,3-dihydroxy-2,6-dimethylheptan-4-yl]-L-leucinamide(Covalent)

2L0.2:	12 residues within 4Å: Chain H: T.1, R.19, S.20, T.21, Q.22, A.27, K.33, G.45, G.47, A.49, G.168 Chain I: D.125 12 PLIP interactions: 10 interactions with chain H, 2 interactions with chain I Hydrophobic interactions: H:Q.22, H:A.27, H:K.33, H:K.33, H:A.49 Hydrogen bonds: H:T.21, H:T.21, H:G.47, H:G.47, H:A.49, I:D.125, I:D.125
2L0.5:	11 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, A.27, K.33, G.47, A.49, Y.170 Chain L: D.126, P.127 13 PLIP interactions: 10 interactions with chain K, 3 interactions with chain L Hydrophobic interactions: K:A.20, K:A.27, L:D.126, L:P.127 Hydrogen bonds: K:T.21, K:T.21, K:T.21, K:G.47, K:G.47, K:A.49, L:D.126 Water bridges: K:T.1, K:S.131
2L0.10:	12 residues within 4Å: Chain Y: T.1, D.17, R.19, A.20, T.21, A.27, K.33, G.47, A.49, Y.170 Chain Z: D.126, P.127 13 PLIP interactions: 10 interactions with chain Y, 3 interactions with chain Z Hydrophobic interactions: Y:A.20, Y:A.27, Z:D.126, Z:P.127 Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:A.49, Y:S.131, Z:D.126 Water bridges: Y:T.1, Y:S.131

1 x 2LR: N-[(benzyloxy)carbonyl]-L-leucyl-N-{(1R,2S)-1-hydroxy-4-methyl-1-[(2R)-2-methyloxiran-2-yl]pentan-2-yl}-L-leucinamide(Covalent)

2LR.8:

15 residues within 4Å:

Chain V: T.1, R.19, S.20, T.21, Q.22, A.27, K.33, G.45, G.47, T.48, A.49, T.52, G.168
Chain W: D.125, C.129

15 PLIP interactions:

12 interactions with chain V, 3 interactions with chain W

Hydrophobic interactions: V:T.1, V:T.21, V:A.27, V:K.33, V:A.49, W:D.125
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

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Stein, M.L. et al., Systematic Comparison of Peptidic Proteasome Inhibitors Highlights the alpha-Ketoamide Electrophile as an Auspicious Reversible Lead Motif. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2014-02-12

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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Background

Transparent

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