SMTL ID : 7pxb.1

Substrate-engaged mycobacterial Proteasome-associated ATPase - focused 3D refinement (state B)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: 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 Chain B: D.401, R.427, R.430 Ligands: MG.2 18 PLIP interactions: 12 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:G.255, A:G.255, A:G.296, A:G.298, A:K.299, A:T.300, A:T.300, A:L.301, A:N.416, A:Q.520, B:D.401, B:R.430 Salt bridges: A:K.299, A:K.299, B:R.427, B:R.427, B:R.427, B:R.430 ATP.3: 19 residues within 4Å: Chain B: 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 E: D.401, R.427, R.430 Ligands: MG.4 18 PLIP interactions: 12 interactions with chain B, 6 interactions with chain E Hydrogen bonds: B:G.255, B:G.255, B:G.296, B:C.297, B:G.298, B:K.299, B:T.300, B:T.300, B:L.301, B:Y.452, E:D.401 Salt bridges: B:K.299, B:K.299, E:R.427, E:R.427, E:R.427, E:R.430, E:R.430 ATP.5: 16 residues within 4Å: Chain C: 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 C Hydrogen bonds: C:D.253, C:G.255, C:G.296, C:G.298, C:T.300, C:T.300, C:T.300, C:L.301 Salt bridges: C:K.299 ATP.7: 16 residues within 4Å: Chain A: R.427 Chain D: D.253, I.254, P.295, C.297, G.298, T.300, L.301, E.372, N.416, I.448, Y.452, G.516, A.517, Q.520 Ligands: MG.8 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:D.253, D:G.298, D:T.300, D:L.301, D:E.372, D:E.372, D:E.372, D:N.416, D:Y.452, D:G.516 ATP.9: 19 residues within 4Å: Chain E: 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 Chain F: D.401, R.427, R.430 Ligands: MG.10 19 PLIP interactions: 14 interactions with chain E, 5 interactions with chain F Hydrogen bonds: E:G.255, E:G.255, E:G.296, E:G.298, E:K.299, E:T.300, E:T.300, E:L.301, E:N.416, E:N.416, E:G.516, E:Q.520 Salt bridges: E:K.299, E:K.299, F:R.427, F:R.427, F:R.427, F:R.430, F:R.430 ATP.11: 17 residues within 4Å: Chain C: R.427, R.430 Chain F: 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.12 15 PLIP interactions: 12 interactions with chain F, 3 interactions with chain C Hydrogen bonds: F:G.255, F:G.255, F:G.296, F:G.298, F:K.299, F:T.300, F:T.300, F:L.301, F:Y.452, F:Q.520, C:R.430 Salt bridges: F:K.299, F:K.299, C:R.427, C:R.427

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.300 Chain B: D.401 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.300 MG.4: 3 residues within 4Å: Chain B: T.300 Chain E: R.430 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.300 MG.6: 3 residues within 4Å: Chain C: T.300, D.371 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain D: G.298, K.299, T.300, D.371 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.300 MG.10: 3 residues within 4Å: Chain E: T.300 Chain F: R.430 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.300 MG.12: 3 residues within 4Å: Chain F: T.300, D.371 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.300

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

AAA ATPase forming ring-shaped complexes: ABCDEF
Prokaryotic ubiquitin-like protein Pup: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

AAA ATPase forming ring-shaped complexes

Prokaryotic ubiquitin-like protein Pup

Related Entries With Identical Sequence