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SMTL ID : 4nnw.1

yCP in complex with Z-Leu-Leu-Leu-ketoaldehyde

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 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 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:D.51
MG.4:	4 residues within 4Å: Chain I: A.175, D.176, D.178, S.181 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:A.175, I:D.178, I:S.181, H₂O.9
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: 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.8:	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: 1 interactions with chain L, 3 interactions with chain V Metal complexes: L:D.222, V:I.163, V:D.166, V:S.169
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.21
MG.13:	4 residues within 4Å: Chain Z: R.28, T.192, H.195, V.198 3 PLIP interactions: 3 interactions with chain Z Metal complexes: Z:T.192, Z:H.195, Z:V.198

6 x 2MK: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2R,3S)-1,2-dihydroxy-5-methylhexan-3-yl]-L-leucinamide(Covalent)

2MK.2:	15 residues within 4Å: Chain H: T.1, S.20, T.21, Q.22, A.27, K.33, A.46, G.47, T.48, A.49, T.52, G.168 Chain I: D.125, L.126, C.129 12 PLIP interactions: 4 interactions with chain I, 8 interactions with chain H Hydrophobic interactions: I:D.125, I:L.126, H:Q.22, H:A.27 Hydrogen bonds: I:D.125, I:D.125, H:T.21, H:T.21, H:G.47, H:G.47, H:A.49 Water bridges: H:A.50
2MK.5:	12 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, A.27, K.33, A.46, G.47, A.49, Y.170 Chain L: D.126, P.127 11 PLIP interactions: 3 interactions with chain L, 8 interactions with chain K Hydrophobic interactions: L:D.126, L:P.127, K:A.20, K:A.27, K:A.49 Hydrogen bonds: L:D.126, K:T.21, K:T.21, K:G.47, K:G.47, K:A.49
2MK.7:	15 residues within 4Å: Chain H: H.114, H.116, S.118 Chain N: T.1, T.20, T.21, T.22, K.33, R.45, S.46, G.47, S.48, A.49, T.52, S.168 10 PLIP interactions: 9 interactions with chain N, 1 interactions with chain H Hydrophobic interactions: N:A.49 Hydrogen bonds: N:T.20, N:T.21, N:T.21, N:G.47, N:G.47, N:G.47, N:A.49 Water bridges: N:A.50, H:H.114
2MK.9:	16 residues within 4Å: Chain V: T.1, S.20, T.21, Q.22, A.27, K.33, G.45, A.46, G.47, T.48, A.49, T.52, G.168 Chain W: D.125, L.126, C.129 12 PLIP interactions: 9 interactions with chain V, 3 interactions with chain W Hydrophobic interactions: V:Q.22, V:A.27, W:L.126 Hydrogen bonds: 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
2MK.11:	11 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, A.27, K.33, G.47, G.48, A.49, Y.170 Chain Z: D.126 10 PLIP interactions: 8 interactions with chain Y, 2 interactions with chain Z Hydrophobic interactions: Y:A.20, Y:A.27, Y:A.49, Z:D.126 Hydrogen bonds: Y:T.21, Y:T.21, Y:G.47, Y:G.47, Y:A.49, Z:D.126
2MK.14:	14 residues within 4Å: Chain 1: T.1, T.20, T.21, T.22, K.33, R.45, G.47, S.48, A.49, T.52, S.168 Chain V: H.114, H.116, S.118 9 PLIP interactions: 9 interactions with chain 1 Hydrophobic interactions: 1:T.22, 1:A.49 Hydrogen bonds: 1:T.20, 1:T.21, 1:T.21, 1:G.47, 1:G.47, 1:G.47, 1:A.49

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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Cartoon
Tube
Trace
Lines
Ball+Stick
Licorice
Hyperball
Rope
Surface
Spacefill
Outline
Fog

Background

Transparent

Resolution

Low
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