SMTL ID : 5mpa.1

26S proteasome in presence of ATP (s2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-1-1-1-1-1-1-mer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain 2: T.257 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:T.257 MG.4: 2 residues within 4Å: Chain 3: T.230 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain 3 Metal complexes: 3:T.230 MG.6: 2 residues within 4Å: Chain 4: T.220 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain 4 Metal complexes: 4:T.220 MG.8: 3 residues within 4Å: Chain 5: T.229, E.282 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain 5 Metal complexes: 5:T.229 MG.10: 2 residues within 4Å: Chain 6: T.229 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain 6 Metal complexes: 6:T.229 MG.12: 3 residues within 4Å: Chain 7: T.196, D.248 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain 7 Metal complexes: 7:T.196

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

ATP.2: 19 residues within 4Å: Chain 2: D.210, G.212, P.252, G.253, T.254, G.255, K.256, T.257, L.258, R.261, E.310, N.356, A.417, R.420 Chain 3: K.214, A.337, R.340, R.343 Ligands: MG.1 19 PLIP interactions: 14 interactions with chain 2, 5 interactions with chain 3 Hydrogen bonds: 2:G.212, 2:G.253, 2:T.254, 2:T.254, 2:G.255, 2:K.256, 2:T.257, 2:L.258, 2:R.261, 2:E.310, 2:N.356, 2:R.420, 3:R.343 Salt bridges: 2:K.256, 2:K.256, 3:R.340, 3:R.340, 3:R.340, 3:R.343 ATP.3: 17 residues within 4Å: Chain 3: D.183, I.184, G.185, G.186, L.187, P.225, G.226, T.227, G.228, K.229, T.230, L.231, I.361, H.365, G.389 Chain 7: R.306 Ligands: MG.4 10 PLIP interactions: 9 interactions with chain 3, 1 interactions with chain 7 Hydrogen bonds: 3:G.186, 3:G.226, 3:T.227, 3:G.228, 3:K.229, 3:T.230, 3:T.230, 3:L.231 Salt bridges: 3:K.229, 7:R.306 ATP.5: 20 residues within 4Å: Chain 4: D.173, G.175, G.176, P.215, G.216, T.217, G.218, K.219, T.220, M.221, E.273, N.319, I.352, T.355, G.380, A.381, A.384 Chain 5: D.313, R.342 Ligands: MG.6 15 PLIP interactions: 14 interactions with chain 4, 1 interactions with chain 5 Hydrogen bonds: 4:G.175, 4:G.176, 4:G.176, 4:P.215, 4:G.218, 4:K.219, 4:T.220, 4:M.221, 4:E.273, 4:N.319, 4:N.319, 4:T.355 Salt bridges: 4:K.219, 4:K.219, 5:R.342 ATP.7: 19 residues within 4Å: Chain 5: G.182, I.183, G.225, T.226, G.227, K.228, T.229, L.230, E.282, N.328, I.360, H.364, G.388, A.389 Chain 6: R.213, A.336, R.339, R.342 Ligands: MG.8 18 PLIP interactions: 11 interactions with chain 5, 7 interactions with chain 6 Hydrogen bonds: 5:G.225, 5:T.226, 5:G.227, 5:K.228, 5:T.229, 5:T.229, 5:L.230, 5:E.282, 5:N.328, 6:R.213, 6:R.342, 6:R.342 Salt bridges: 5:K.228, 5:K.228, 6:R.339, 6:R.339, 6:R.339, 6:R.342 ATP.9: 15 residues within 4Å: Chain 2: R.367, R.370 Chain 6: V.183, G.184, P.224, G.225, T.226, G.227, K.228, T.229, L.230, N.328, I.360, H.364 Ligands: MG.10 14 PLIP interactions: 10 interactions with chain 6, 4 interactions with chain 2 Hydrogen bonds: 6:G.184, 6:G.225, 6:T.226, 6:T.226, 6:G.227, 6:K.228, 6:T.229, 6:L.230 Salt bridges: 6:K.228, 6:K.228, 2:R.367, 2:R.367, 2:R.367, 2:R.370

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

ADP.11: 14 residues within 4Å: Chain 7: M.149, V.150, P.191, G.192, T.193, G.194, K.195, T.196, L.197, I.327, G.355, A.356, K.359 Ligands: MG.12 7 PLIP interactions: 7 interactions with chain 7 Hydrogen bonds: 7:V.150, 7:G.192, 7:G.194, 7:K.195, 7:T.196, 7:L.197 Salt bridges: 7:K.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wehmer, M. et al., Structural insights into the functional cycle of the ATPase module of the 26S proteasome. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-03-08

Peptides

Proteasome subunit alpha type-1: AO
Proteasome subunit alpha type-2: BP
Proteasome subunit alpha type-3: CQ
Proteasome subunit alpha type-4: DR
Proteasome subunit alpha type-5: ES
Proteasome subunit alpha type-6: FT
Probable proteasome subunit alpha type-7: GU
Proteasome subunit beta type-1: HV
Proteasome subunit beta type-2: IW
Proteasome subunit beta type-3: JX
Proteasome subunit beta type-4: KY
Proteasome subunit beta type-5: LZ
Proteasome subunit beta type-6: M0
Proteasome subunit beta type-7: N1
26S protease regulatory subunit 7 homolog: 2
26S protease regulatory subunit 4 homolog: 3
26S protease regulatory subunit 6B homolog: 4
26S protease subunit RPT4: 5
26S protease regulatory subunit 6A: 6
26S protease regulatory subunit 8 homolog: 7

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
a

O
A

B
b

P
B

C
c

Q
C

D
d

R
D

E
e

S
E

F
f

T
F

G
g

U
G

H
h

V
1

I
i

W
2

J
j

X
3

K
k

Y
4

L
l

Z
5

M
m

0
6

N
n

1
7

2
H

3
I

4
K

5
L

6
M

7
J

Proteasome subunit alpha type-1

Proteasome subunit alpha type-2

Proteasome subunit alpha type-3

Proteasome subunit alpha type-4

Proteasome subunit alpha type-5

Proteasome subunit alpha type-6

Probable proteasome subunit alpha type-7

Proteasome subunit beta type-1

Proteasome subunit beta type-2

Proteasome subunit beta type-3

Proteasome subunit beta type-4

Proteasome subunit beta type-5

Proteasome subunit beta type-6

Proteasome subunit beta type-7

26S protease regulatory subunit 7 homolog

26S protease regulatory subunit 4 homolog

26S protease regulatory subunit 6B homolog

26S protease subunit RPT4

26S protease regulatory subunit 6A

26S protease regulatory subunit 8 homolog

Related Entries With Identical Sequence