SMTL ID : 5mpc.1

26S proteasome in presence of BeFx (s4)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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

ATP.1: 19 residues within 4Å: Chain 2: G.212, K.215, P.251, P.252, G.253, T.254, G.255, K.256, T.257, L.258, N.356, I.388, H.392, G.416, A.417, R.420 Chain 3: D.314, R.343 Ligands: MG.2 17 PLIP interactions: 14 interactions with chain 2, 3 interactions with chain 3 Hydrogen bonds: 2:G.212, 2:G.212, 2:K.215, 2:G.253, 2:T.254, 2:T.254, 2:G.255, 2:K.256, 2:T.257, 2:T.257, 2:L.258, 2:N.356, 3:D.314 Salt bridges: 2:K.256, 2:K.256, 3:R.343, 3:R.343 ATP.3: 19 residues within 4Å: Chain 3: G.186, A.224, P.225, G.226, T.227, G.228, K.229, T.230, L.231, L.232, I.361, G.389, A.390 Chain 7: R.270, E.274, P.307, G.308, R.309 Ligands: MG.4 8 PLIP interactions: 5 interactions with chain 3, 3 interactions with chain 7 Hydrogen bonds: 3:G.226, 3:T.227, 3:G.228, 3:K.229, 3:T.230, 7:E.274, 7:G.308 Salt bridges: 7:R.270 ATP.9: 18 residues within 4Å: Chain 2: D.341, R.367, P.368, R.370 Chain 6: G.184, P.224, G.225, T.226, G.227, K.228, T.229, E.282, N.328, I.360, H.364, G.388, A.389 Ligands: MG.10 15 PLIP interactions: 4 interactions with chain 2, 11 interactions with chain 6 Hydrogen bonds: 2:D.341, 2:R.367, 6:G.184, 6:G.184, 6:G.225, 6:T.226, 6:G.227, 6:K.228, 6:T.229, 6:E.282, 6:N.328 Salt bridges: 2:R.370, 2:R.370, 6:K.228, 6:K.228 ATP.11: 22 residues within 4Å: Chain 4: R.207, D.304, L.328, R.333 Chain 7: M.149, V.150, P.190, P.191, G.192, T.193, G.194, K.195, T.196, L.197, I.250, N.295, I.327, H.331, G.355, A.356, K.359 Ligands: MG.12 14 PLIP interactions: 10 interactions with chain 7, 4 interactions with chain 4 Hydrogen bonds: 7:G.192, 7:T.193, 7:T.193, 7:G.194, 7:K.195, 7:T.196, 7:T.196, 7:K.359, 4:R.207, 4:D.304, 4:R.333 Salt bridges: 7:K.195, 7:K.195, 4:R.333

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain 2: T.257 Chain 3: D.314 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain 2 Metal complexes: 2:T.257 MG.4: 3 residues within 4Å: Chain 3: T.230 Chain 7: E.274 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: ADP.5 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain 5: T.229, D.281 Ligands: ADP.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: 2 residues within 4Å: Chain 7: T.196 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain 7 Metal complexes: 7:T.196

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

ADP.5: 14 residues within 4Å: Chain 4: V.174, G.175, G.176, L.177, P.215, G.216, T.217, G.218, K.219, T.220, M.221, G.380, A.381 Ligands: MG.6 12 PLIP interactions: 12 interactions with chain 4 Hydrogen bonds: 4:G.175, 4:G.176, 4:G.176, 4:G.216, 4:T.217, 4:T.217, 4:G.218, 4:K.219, 4:T.220, 4:T.220, 4:M.221 Salt bridges: 4:K.219 ADP.7: 14 residues within 4Å: Chain 5: G.182, I.183, G.184, P.224, G.225, T.226, G.227, K.228, T.229, N.328, I.360, G.388, A.389 Ligands: MG.8 9 PLIP interactions: 9 interactions with chain 5 Hydrogen bonds: 5:G.184, 5:G.225, 5:T.226, 5:T.226, 5:G.227, 5:K.228, 5:T.229, 5:N.328 Salt bridges: 5:K.228

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
26S proteasome regulatory subunit RPN10: 8
Ubiquitin carboxyl-terminal hydrolase RPN11: 9
26S proteasome regulatory subunit RPN12: a
26S proteasome regulatory subunit RPN13: b
26S proteasome complex subunit SEM1: c
26S proteasome regulatory subunit RPN1: d
26S proteasome regulatory subunit RPN2: e
26S proteasome regulatory subunit RPN3: f
26S proteasome regulatory subunit RPN5: g
26S proteasome regulatory subunit RPN6: h
26S proteasome regulatory subunit RPN7: i
26S proteasome regulatory subunit RPN8: j
26S proteasome regulatory subunit RPN9: k
Ubiquitin carboxyl-terminal hydrolase 6: l

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

8
W

9
V

a
T

b
X

c
Y

d
Z

e
N

f
S

g
P

h
Q

i
R

j
U

k
O

l
8

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

26S proteasome regulatory subunit RPN10

Ubiquitin carboxyl-terminal hydrolase RPN11

26S proteasome regulatory subunit RPN12

26S proteasome regulatory subunit RPN13

26S proteasome complex subunit SEM1

26S proteasome regulatory subunit RPN1

26S proteasome regulatory subunit RPN2

26S proteasome regulatory subunit RPN3

26S proteasome regulatory subunit RPN5

26S proteasome regulatory subunit RPN6

26S proteasome regulatory subunit RPN7

26S proteasome regulatory subunit RPN8

26S proteasome regulatory subunit RPN9

Ubiquitin carboxyl-terminal hydrolase 6

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