SMTL ID : 6hed.1

PAN-proteasome in state 5

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-14-6-mer

Ligands

4 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 19 residues within 4Å: Chain 2: L.138, P.176, G.177, T.178, G.179, K.180, T.181, L.182, E.234, N.280, I.312, H.316, G.340, A.341, K.344 Chain 3: A.288, R.291, R.294 Ligands: MG.2 15 PLIP interactions: 5 interactions with chain 3, 10 interactions with chain 2 Hydrogen bonds: 3:A.288, 2:G.177, 2:T.178, 2:T.178, 2:G.179, 2:K.180, 2:T.181, 2:T.181, 2:T.181 Salt bridges: 3:R.291, 3:R.291, 3:R.291, 3:R.294, 2:K.180, 2:K.180 ATP.5: 24 residues within 4Å: Chain 4: I.135, G.136, G.137, P.176, G.177, T.178, G.179, K.180, T.181, L.182, E.234, N.280, I.312, H.316, G.340, A.341, K.344 Chain 5: L.261, D.265, G.266, R.291, G.293, R.294 Ligands: MG.6 18 PLIP interactions: 11 interactions with chain 4, 7 interactions with chain 5 Hydrogen bonds: 4:G.136, 4:G.136, 4:G.177, 4:T.178, 4:G.179, 4:K.180, 4:T.181, 4:T.181, 4:N.280, 5:D.265 Salt bridges: 4:K.180, 4:K.180, 5:R.291, 5:R.291, 5:R.291, 5:R.294, 5:R.294, 5:R.294 ATP.7: 21 residues within 4Å: Chain 5: I.135, G.137, P.176, G.177, T.178, G.179, K.180, T.181, L.182, N.280, I.312, H.316, G.340, A.341, K.344 Chain 6: L.261, G.266, A.288, R.291, R.294 Ligands: MG.8 17 PLIP interactions: 7 interactions with chain 6, 10 interactions with chain 5 Hydrogen bonds: 6:D.265, 6:R.291, 5:G.137, 5:G.177, 5:T.178, 5:G.179, 5:K.180, 5:T.181, 5:T.181, 5:L.182 Salt bridges: 6:R.291, 6:R.291, 6:R.294, 6:R.294, 6:R.294, 5:K.180, 5:K.180 ATP.9: 19 residues within 4Å: Chain 2: L.261, D.265, R.291, G.293, R.294 Chain 6: P.176, G.177, T.178, G.179, K.180, T.181, L.182, E.234, N.280, I.312, G.340, A.341, K.344 Ligands: MG.10 14 PLIP interactions: 6 interactions with chain 2, 8 interactions with chain 6 Hydrogen bonds: 2:D.265, 2:G.293, 6:G.177, 6:T.178, 6:K.180, 6:T.181, 6:T.181, 6:T.181 Salt bridges: 2:R.291, 2:R.291, 2:R.291, 2:R.294, 6:K.180, 6:K.180

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain 2: T.181 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain 3: T.181 Ligands: ADP.3 1 PLIP interactions: 1 interactions with chain 3 Metal complexes: 3:T.181 MG.6: 3 residues within 4Å: Chain 4: T.181 Chain 5: R.294 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain 4 Metal complexes: 4:T.181 MG.8: 2 residues within 4Å: Chain 5: T.181 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain 5 Metal complexes: 5:T.181 MG.10: 2 residues within 4Å: Chain 6: T.181 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain 6 Metal complexes: 6:T.181

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)

ADP.3: 17 residues within 4Å: Chain 3: I.135, G.136, G.177, T.178, G.179, K.180, T.181, L.182, I.312, H.316, G.340, A.341, K.344 Chain 7: K.168, D.265, R.294 Ligands: MG.4 13 PLIP interactions: 10 interactions with chain 3, 3 interactions with chain 7 Hydrogen bonds: 3:G.177, 3:T.178, 3:T.178, 3:G.179, 3:K.180, 3:T.181, 3:T.181, 3:T.181, 3:L.182, 7:D.265, 7:D.265, 7:R.294 Salt bridges: 3:K.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Majumder, P. et al., Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2018-12-26

Peptides

Proteasome subunit alpha: ABCDEFGHIJKLMN
Proteasome subunit beta: OPQRSTUVWXYZ01
Proteasome-activating nucleotidase: 234567

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
a

C
B

D
b

E
C

F
c

G
D

H
d

I
E

J
e

K
F

L
f

M
G

N
g

O
1

P
h

Q
2

R
i

S
3

T
j

U
4

V
k

W
5

X
l

Y
6

Z
m

0
7

1
n

2
H

3
I

4
K

5
L

6
M

7
J

Proteasome subunit alpha

Proteasome subunit beta

Proteasome-activating nucleotidase

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