SMTL ID : 5a0q.1

Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.50 Å

Oligo State

hetero-oligomer

Ligands

6 x KNM: ADA-(AHX)3-(LEU)3-VINYL SULFONE(Covalent)

KNM.1: 15 residues within 4Å: Chain H: T.1, T.20, T.21, T.22, K.33, R.45, S.46, G.47, S.48, A.49, G.129, S.130 Chain I: Y.114, H.116, S.118 10 PLIP interactions: 9 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:T.1, H:T.20, H:T.22, H:K.33, H:R.45, H:A.49, I:Y.114 Hydrogen bonds: H:T.21, H:T.22, H:A.49 KNM.2: 12 residues within 4Å: Chain I: T.1, A.20, T.21, E.22, K.33, A.46, G.47, A.49, T.52, G.128, S.129 Chain J: D.124 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:T.1, I:A.20, I:E.22, I:K.33, I:A.49, I:T.52 Hydrogen bonds: I:G.47, I:A.49 KNM.3: 10 residues within 4Å: Chain L: T.1, A.20, T.21, A.22, K.33, M.45, G.47, G.48, A.49 Chain M: D.125 10 PLIP interactions: 8 interactions with chain L, 2 interactions with chain M Hydrophobic interactions: L:A.20, L:T.21, L:A.22, L:K.33, L:A.49 Hydrogen bonds: L:T.21, L:T.21, L:G.47, M:D.125, M:D.125 KNM.4: 15 residues within 4Å: Chain V: T.1, T.20, T.21, T.22, K.33, R.45, S.46, G.47, S.48, A.49, G.129, S.130 Chain W: Y.114, H.116, S.118 10 PLIP interactions: 9 interactions with chain V, 1 interactions with chain W Hydrophobic interactions: V:T.1, V:T.20, V:T.22, V:K.33, V:R.45, V:A.49, W:Y.114 Hydrogen bonds: V:T.21, V:T.22, V:A.49 KNM.5: 12 residues within 4Å: Chain W: T.1, A.20, T.21, E.22, K.33, A.46, G.47, A.49, T.52, G.128, S.129 Chain X: D.124 8 PLIP interactions: 8 interactions with chain W Hydrophobic interactions: W:T.1, W:A.20, W:E.22, W:K.33, W:A.49, W:T.52 Hydrogen bonds: W:G.47, W:A.49 KNM.6: 10 residues within 4Å: Chain 0: D.125 Chain Z: T.1, A.20, T.21, A.22, K.33, M.45, G.47, G.48, A.49 10 PLIP interactions: 2 interactions with chain 0, 8 interactions with chain Z Hydrogen bonds: 0:D.125, 0:D.125, Z:T.21, Z:T.21, Z:G.47 Hydrophobic interactions: Z:A.20, Z:T.21, Z:A.22, Z:K.33, Z:A.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Da Fonseca, P.C.A. et al., Cryo-Em Reveals the Conformation of a Substrate Analogue in the Human 20S Proteasome Core. Nat.Commun. (2015)

Release Date

2015-12-30

Peptides

PROTEASOME SUBUNIT ALPHA TYPE-6: AO
PROTEASOME SUBUNIT ALPHA TYPE-2: BP
PROTEASOME SUBUNIT ALPHA TYPE-4: CQ
PROTEASOME SUBUNIT ALPHA TYPE-7: DR
PROTEASOME SUBUNIT ALPHA TYPE-5: ES
PROTEASOME SUBUNIT ALPHA TYPE-1: FT
PROTEASOME SUBUNIT ALPHA TYPE-3: GU
PROTEASOME SUBUNIT BETA TYPE-6: HV
PROTEASOME SUBUNIT BETA TYPE-7: IW
PROTEASOME SUBUNIT BETA TYPE-3: JX
PROTEASOME SUBUNIT BETA TYPE-2: KY
PROTEASOME SUBUNIT BETA TYPE-5: LZ
PROTEASOME SUBUNIT BETA TYPE-1: M0
PROTEASOME SUBUNIT BETA TYPE-4: 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

PROTEASOME SUBUNIT ALPHA TYPE-6

PROTEASOME SUBUNIT ALPHA TYPE-2

PROTEASOME SUBUNIT ALPHA TYPE-4

PROTEASOME SUBUNIT ALPHA TYPE-7

PROTEASOME SUBUNIT ALPHA TYPE-5

PROTEASOME SUBUNIT ALPHA TYPE-1

PROTEASOME SUBUNIT ALPHA TYPE-3

PROTEASOME SUBUNIT BETA TYPE-6

PROTEASOME SUBUNIT BETA TYPE-7

PROTEASOME SUBUNIT BETA TYPE-3

PROTEASOME SUBUNIT BETA TYPE-2

PROTEASOME SUBUNIT BETA TYPE-5

PROTEASOME SUBUNIT BETA TYPE-1

PROTEASOME SUBUNIT BETA TYPE-4

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