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SMTL ID : 6hw4.1

Yeast 20S proteasome in complex with 16

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 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.17, G:M.134
MG.4:	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.5:	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: 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.7:	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.8:	7 residues within 4Å: Chain L: D.222 Chain V: G.162, I.163, W.164, D.166, L.167, S.169 3 PLIP interactions: 1 interactions with chain L, 2 interactions with chain V Metal complexes: L:D.222, V:I.163, V:D.166
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.12:	3 residues within 4Å: Chain X: Q.118, D.120, T.124 No protein-ligand interaction detected (PLIP)
MG.14:	6 residues within 4Å: Chain Z: R.28, T.192, H.195, I.196, 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.2:	3 residues within 4Å: Chain G: R.120, N.123 Chain H: Y.69 Ligand excluded by PLIP
CL.10:	3 residues within 4Å: Chain U: R.120, N.123 Chain V: Y.69 Ligand excluded by PLIP

4 x GRW: (2~{S})-~{N}-[(2~{S},3~{R})-1-[[(2~{S})-1-[4-(aminomethyl)phenyl]-4-methylsulfonyl-butan-2-yl]amino]-3-oxidanyl-1-oxidanylidene-butan-2-yl]-2-[[(2~{R})-2-azido-3-phenyl-propanoyl]amino]-4-methyl-pentanamide(Covalent)

GRW.3:	19 residues within 4Å: Chain H: T.1, S.20, T.21, Q.22, A.27, C.31, A.32, K.33, H.35, G.45, G.47, T.48, A.49, E.53, G.128, S.129 Chain I: D.125, L.126, C.129 17 PLIP interactions: 4 interactions with chain I, 13 interactions with chain H Hydrophobic interactions: I:D.125, I:L.126, H:T.1, H:A.27, H:T.48, H:A.49 Hydrogen bonds: I:D.125, I:D.125, H:T.21, H:T.21, H:T.21, H:T.21, H:Q.22, H:G.47, H:A.49, H:E.53, H:E.53
GRW.6:	19 residues within 4Å: Chain K: T.1, R.19, A.20, T.21, A.22, A.27, V.31, K.33, M.45, G.47, A.49, Q.53, G.130, S.131 Chain L: Y.106, D.126, P.127, V.128, S.130 19 PLIP interactions: 13 interactions with chain K, 6 interactions with chain L Hydrophobic interactions: K:A.22, K:A.27, K:V.31, K:K.33, K:K.33, K:M.45, K:A.49, L:Y.106, L:D.126, L:P.127, L:V.128 Hydrogen bonds: K:T.21, K:T.21, K:T.21, K:G.47, K:A.49, L:D.126, L:S.130 Water bridges: K:K.32
GRW.11:	18 residues within 4Å: Chain V: T.1, S.20, T.21, Q.22, A.27, C.31, K.33, H.35, G.45, G.47, T.48, A.49, E.53, G.128, S.129 Chain W: D.125, L.126, C.129 20 PLIP interactions: 16 interactions with chain V, 4 interactions with chain W Hydrophobic interactions: V:T.1, V:Q.22, V:A.27, V:K.33, V:K.33, V:T.48, V:A.49, W:D.125, W:L.126 Hydrogen bonds: V:T.21, V:T.21, V:T.21, V:T.21, V:Q.22, V:A.32, V:G.47, V:A.49, V:E.53, W:D.125, W:D.125
GRW.13:	19 residues within 4Å: Chain Y: T.1, R.19, A.20, T.21, A.22, A.27, V.31, K.33, M.45, G.47, A.49, Q.53, G.130, S.131 Chain Z: Y.106, D.126, P.127, V.128, S.130 17 PLIP interactions: 5 interactions with chain Z, 12 interactions with chain Y Hydrophobic interactions: Z:Y.106, Z:D.126, Z:V.128, Y:A.22, Y:A.27, Y:V.31, Y:K.33, Y:K.33, Y:M.45, Y:A.49 Hydrogen bonds: Z:D.126, Z:S.130, Y:T.21, Y:T.21, Y:T.21, Y:G.47, Y:A.49

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Xin, B.T. et al., Structure-Based Design of Inhibitors Selective for Human Proteasome beta 2c or beta 2i Subunits. J.Med.Chem. (2019)

Release Date

2019-01-30

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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Extreme

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