SMTL ID : 5mp9.1

26S proteasome in presence of ATP (s1)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-oligomer

Ligands

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

ATP.1: 20 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, N.356, I.388, H.392, G.416, A.417, R.420 Chain 3: D.314, R.340, R.343 Ligands: MG.2 14 PLIP interactions: 3 interactions with chain 3, 11 interactions with chain 2 Salt bridges: 3:R.340, 3:R.340, 3:R.343, 2:K.256, 2:K.256 Hydrogen bonds: 2:G.212, 2:G.253, 2:T.254, 2:G.255, 2:K.256, 2:T.257, 2:T.257, 2:L.258, 2:R.261 ATP.3: 18 residues within 4Å: Chain 3: D.183, I.184, G.185, L.187, P.225, G.226, T.227, G.228, K.229, T.230, L.231, I.361, H.365, G.389, A.390, Q.393 Chain 7: R.306 Ligands: MG.4 14 PLIP interactions: 11 interactions with chain 3, 3 interactions with chain 7 Hydrogen bonds: 3:G.185, 3:G.226, 3:T.227, 3:G.228, 3:K.229, 3:T.230, 3:T.230, 3:L.231, 3:Q.393 Salt bridges: 3:K.229, 3:K.229, 7:R.306, 7:R.306, 7:R.306 ATP.5: 17 residues within 4Å: Chain 4: D.173, V.174, G.175, G.176, P.215, G.216, T.217, G.218, K.219, T.220, M.221, N.319, G.380, A.381, A.384 Chain 5: R.342 Ligands: MG.6 12 PLIP interactions: 10 interactions with chain 4, 2 interactions with chain 5 Hydrogen bonds: 4:G.175, 4:G.176, 4:G.216, 4:T.217, 4:G.218, 4:K.219, 4:T.220, 4:M.221 Salt bridges: 4:K.219, 4:K.219, 5:R.339, 5:R.342 ATP.7: 20 residues within 4Å: Chain 5: G.184, L.186, P.224, G.225, T.226, G.227, K.228, T.229, L.230, E.282, N.328, I.360, H.364, G.388, A.389, R.392 Chain 6: D.313, R.339, R.342 Ligands: MG.8 15 PLIP interactions: 11 interactions with chain 5, 4 interactions with chain 6 Hydrogen bonds: 5:G.184, 5:G.184, 5:G.225, 5:G.227, 5:K.228, 5:T.229, 5:T.229, 5:T.229, 5:L.230, 6:R.213 Salt bridges: 5:K.228, 5:K.228, 6:R.339, 6:R.339, 6:R.342 ATP.9: 20 residues within 4Å: Chain 2: D.341, R.367, R.370 Chain 6: G.184, L.186, P.224, G.225, T.226, G.227, K.228, T.229, L.230, E.282, N.328, I.360, H.364, G.388, A.389, K.392 Ligands: MG.10 17 PLIP interactions: 13 interactions with chain 6, 4 interactions with chain 2 Hydrogen bonds: 6:G.184, 6:G.184, 6:G.225, 6:T.226, 6:G.227, 6:K.228, 6:T.229, 6:T.229, 6:T.229, 6:L.230, 6:N.328, 2:R.370 Salt bridges: 6:K.228, 6:K.228, 2:R.367, 2:R.367, 2:R.370

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain 2: T.257 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Chain 3: T.230 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) 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: 2 residues within 4Å: Chain 5: T.229 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain 6: T.229, D.281 Ligands: ATP.9 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain 7: T.196 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain 7 Metal complexes: 7:T.196

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.11: 17 residues within 4Å: Chain 7: M.149, V.150, L.153, P.191, G.192, T.193, G.194, K.195, T.196, L.197, R.200, I.327, H.331, G.355, A.356, K.359 Ligands: MG.12 11 PLIP interactions: 11 interactions with chain 7 Hydrogen bonds: 7:V.150, 7:G.192, 7:G.194, 7:K.195, 7:T.196, 7:T.196, 7:L.197, 7:R.200, 7:K.359 Salt bridges: 7:K.195, 7:R.200

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

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