SMTL ID : 6he4.1

AAA-ATPase ring of PAN-proteasomes

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: I.21, G.22, G.63, T.64, G.65, K.66, T.67, L.68, N.166, I.198, H.202, G.226, A.227, K.230 Chain B: K.54, L.147, A.174, R.177, R.180 Ligands: MG.2 16 PLIP interactions: 5 interactions with chain B, 11 interactions with chain A Hydrogen bonds: B:R.177, A:G.22, A:G.22, A:G.63, A:T.64, A:G.65, A:K.66, A:T.67, A:T.67, A:N.166 Salt bridges: B:R.177, B:R.180, B:R.180, B:R.180, A:K.66, A:K.66 ATP.3: 22 residues within 4Å: Chain B: I.21, G.22, G.23, P.62, G.63, T.64, G.65, K.66, T.67, L.68, N.166, I.198, H.202, G.226, A.227 Chain F: L.147, D.151, G.152, A.174, R.177, R.180 Ligands: MG.4 17 PLIP interactions: 10 interactions with chain B, 7 interactions with chain F Hydrogen bonds: B:G.22, B:G.63, B:T.64, B:G.65, B:K.66, B:T.67, B:T.67, B:L.68, F:G.152, F:A.174 Salt bridges: B:K.66, B:K.66, F:R.177, F:R.177, F:R.180, F:R.180, F:R.180 ATP.5: 21 residues within 4Å: Chain C: L.24, P.62, G.63, T.64, G.65, K.66, T.67, L.68, E.120, N.166, I.198, I.201, H.202, G.226, A.227, K.230 Chain D: D.151, A.174, R.177, R.180 Ligands: MG.6 17 PLIP interactions: 10 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:G.63, C:T.64, C:T.64, C:G.65, C:K.66, C:T.67, C:T.67, C:N.166, D:D.151, D:D.151, D:A.174 Salt bridges: C:K.66, C:K.66, D:R.177, D:R.177, D:R.177, D:R.180 ATP.9: 21 residues within 4Å: Chain C: K.54, L.147, D.151, R.177, R.180 Chain F: G.22, P.61, P.62, G.63, T.64, G.65, K.66, T.67, L.68, E.120, I.198, H.202, G.226, A.227, K.230 Ligands: MG.10 17 PLIP interactions: 11 interactions with chain F, 6 interactions with chain C Hydrogen bonds: F:G.63, F:T.64, F:T.64, F:K.66, F:T.67, F:T.67, F:T.67, F:L.68, F:K.230, C:K.54, C:D.151, C:R.180 Salt bridges: F:K.66, F:K.66, C:R.177, C:R.177, C:R.177

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.67 Chain B: R.180 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.67 MG.4: 3 residues within 4Å: Chain B: T.67 Chain F: R.180 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain C: T.67, E.120 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain D: T.67 Ligands: ADP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.67 MG.10: 2 residues within 4Å: Chain F: T.67 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.67

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

ADP.7: 16 residues within 4Å: Chain D: I.21, G.22, G.63, T.64, G.65, K.66, T.67, L.68, I.198, H.202, G.226, A.227, K.230 Chain E: E.51, D.151 Ligands: MG.8 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:G.22, D:G.63, D:G.65, D:K.66, D:T.67, D:T.67, E:K.54, E:K.54 Salt bridges: D:K.66

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Majumder, P. et al., Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle. Proc. Natl. Acad. Sci. U.S.A. (2019)

Release Date

2018-12-26

Peptides

Proteasome-activating nucleotidase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
K

D
L

E
M

F
J

Proteasome-activating nucleotidase