SMTL ID : 7pxc.1

Substrate-engaged mycobacterial Proteasome-associated ATPase in complex with open-gate 20S CP - composite map (state A)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-14-7-1-14-mer

Ligands

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

ATP.1: 17 residues within 4Å: Chain G: I.254, G.255, P.295, G.296, C.297, G.298, K.299, T.300, L.301, N.416, I.448, Y.452, A.517, Q.520 Chain H: R.427, R.430 Ligands: MG.2 16 PLIP interactions: 12 interactions with chain G, 4 interactions with chain H Hydrogen bonds: G:G.255, G:G.255, G:G.296, G:G.298, G:K.299, G:T.300, G:T.300, G:L.301, G:N.416, G:N.416 Salt bridges: G:K.299, G:K.299, H:R.427, H:R.427, H:R.427, H:R.430 ATP.3: 20 residues within 4Å: Chain H: I.254, G.255, P.295, G.296, C.297, G.298, K.299, T.300, L.301, E.372, N.416, I.448, Y.452, G.516, A.517, Q.520 Chain K: D.401, R.427, R.430 Ligands: MG.4 19 PLIP interactions: 13 interactions with chain H, 6 interactions with chain K Hydrogen bonds: H:G.255, H:G.255, H:G.296, H:C.297, H:G.298, H:K.299, H:T.300, H:T.300, H:L.301, H:Y.452, H:Q.520, K:D.401 Salt bridges: H:K.299, H:K.299, K:R.427, K:R.427, K:R.427, K:R.430, K:R.430 ATP.5: 16 residues within 4Å: Chain I: D.253, I.254, G.255, P.295, G.296, C.297, G.298, K.299, T.300, L.301, I.448, Y.452, G.516, A.517, Q.520 Ligands: MG.6 9 PLIP interactions: 9 interactions with chain I Hydrogen bonds: I:G.255, I:G.255, I:G.296, I:G.298, I:K.299, I:T.300, I:T.300, I:L.301 Salt bridges: I:K.299 ATP.8: 17 residues within 4Å: Chain K: G.255, P.295, G.296, C.297, G.298, K.299, T.300, L.301, E.372, I.448, Y.452, G.516, A.517 Chain L: D.401, R.427, R.430 Ligands: MG.9 17 PLIP interactions: 6 interactions with chain L, 11 interactions with chain K Hydrogen bonds: L:D.401, K:G.255, K:G.255, K:G.296, K:G.298, K:K.299, K:T.300, K:T.300, K:L.301, K:E.372 Salt bridges: L:R.427, L:R.427, L:R.427, L:R.430, L:R.430, K:K.299, K:K.299 ATP.10: 19 residues within 4Å: Chain I: R.427, R.430 Chain L: D.253, I.254, G.255, P.295, G.296, C.297, G.298, K.299, T.300, L.301, N.416, I.448, Y.452, G.516, A.517, Q.520 Ligands: MG.11 17 PLIP interactions: 12 interactions with chain L, 5 interactions with chain I Hydrogen bonds: L:G.255, L:G.255, L:G.296, L:G.298, L:K.299, L:T.300, L:L.301, L:N.416, L:Y.452, L:Q.520, I:D.401 Salt bridges: L:K.299, L:K.299, I:R.427, I:R.427, I:R.427, I:R.430

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain G: T.300 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.300 MG.4: 4 residues within 4Å: Chain H: T.300 Chain K: D.401, R.430 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.300 MG.6: 2 residues within 4Å: Chain I: T.300 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.300 MG.9: 4 residues within 4Å: Chain K: T.300, E.372 Chain L: R.430 Ligands: ATP.8 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.300 MG.11: 3 residues within 4Å: Chain L: T.300, E.372 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.300

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

ADP.7: 15 residues within 4Å: Chain J: D.253, I.254, G.255, G.296, C.297, G.298, K.299, T.300, L.301, I.448, K.451, Y.452, G.516, A.517, Q.520 9 PLIP interactions: 9 interactions with chain J Hydrogen bonds: J:G.255, J:G.255, J:C.297, J:K.299, J:T.300, J:T.300, J:L.301, J:Y.452, J:Q.520

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kavalchuk, M. et al., Structural basis of prokaryotic ubiquitin-like protein engagement and translocation by the mycobacterial Mpa-proteasome complex. Nat Commun (2022)

Release Date

2022-01-19

Peptides

Proteasome subunit alpha: ACDEFOQUWZ3589
Proteasome-associated ATPase: BGHIJKL
Prokaryotic ubiquitin-like protein Pup: M
Proteasome subunit beta: NPRSTVXY012467

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

C
2

D
4

E
6

F
8

O
I

Q
K

U
O

W
Q

Z
T

3
X

5
Z

8
d

9
f

B
1

G
A

H
B

I
C

J
D

K
E

L
F

M
G

N
H

P
J

R
L

S
M

T
N

V
P

X
R

Y
S

0
U

1
V

2
W

4
Y

6
a

7
b

Proteasome subunit alpha

Proteasome-associated ATPase

Prokaryotic ubiquitin-like protein Pup

Proteasome subunit beta

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