SMTL ID : 6nyy.1

human m-AAA protease AFG3L2, substrate-bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-4-mer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.306, Q.307, H.310, D.381 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.306, A:D.381 ZN.4: 4 residues within 4Å: Chain B: H.306, H.310, D.381 Chain H: A.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.306, B:H.310, B:D.381 ZN.6: 5 residues within 4Å: Chain C: H.306, H.310, D.381 Chain I: A.5, A.6 5 PLIP interactions: 1 interactions with chain I, 4 interactions with chain C Metal complexes: I:A.5, C:H.306, C:H.310, C:D.381, C:D.381 ZN.10: 5 residues within 4Å: Chain D: H.306, H.310, D.381 Chain J: A.5, A.6 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain J Metal complexes: D:H.306, D:H.310, D:D.381, D:D.381, J:A.5 ZN.12: 3 residues within 4Å: Chain E: H.306, H.310, D.381 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.306, E:D.381 ZN.13: 3 residues within 4Å: Chain F: H.306, H.310, D.381 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.306, F:H.310, F:D.381

3 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)(Covalent)

ANP.2: 20 residues within 4Å: Chain B: D.41, V.42, P.81, P.82, G.83, T.84, G.85, K.86, T.87, L.88, Q.140, N.186, I.218, H.222, G.250, A.254 Chain C: D.171, R.197, R.200 Ligands: MG.3 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:G.83, B:T.84, B:T.84, B:G.85, B:K.86, B:K.86, B:K.86, B:T.87, B:T.87, B:L.88, B:Q.140, C:R.197, C:R.200, C:R.200 Salt bridges: C:R.197 ANP.7: 18 residues within 4Å: Chain C: D.41, A.43, P.82, G.83, T.84, G.85, K.86, T.87, L.88, Q.140, I.218, H.222, G.250, A.251 Chain D: D.171, R.197, R.200 Ligands: MG.5 12 PLIP interactions: 3 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:R.197, D:R.200, C:A.43, C:A.43, C:G.83, C:T.84, C:K.86, C:T.87, C:T.87, C:L.88, C:Q.140 Salt bridges: D:R.197 ANP.8: 21 residues within 4Å: Chain D: D.41, V.42, A.43, P.82, G.83, T.84, G.85, K.86, T.87, L.88, Q.140, N.186, I.218, H.222, G.250, A.251, A.254 Chain E: D.171, R.197, R.200 Ligands: MG.9 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:A.43, D:A.43, D:G.83, D:T.84, D:T.84, D:G.85, D:K.86, D:K.86, D:T.87, D:T.87, D:L.88, D:Q.140, D:N.186, E:R.197, E:R.197 Salt bridges: E:R.197

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain B: T.87, D.139 Ligands: ANP.2 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.87 MG.5: 2 residues within 4Å: Chain C: T.87 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.87 MG.9: 4 residues within 4Å: Chain D: T.87, D.139 Chain E: D.171 Ligands: ANP.8 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.87

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

ADP.11: 14 residues within 4Å: Chain E: D.41, A.43, G.83, T.84, G.85, K.86, T.87, L.88, D.139, I.218, H.222, G.250, A.251, A.254 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:A.43, E:A.43, E:G.83, E:G.85, E:K.86, E:T.87, E:T.87, E:D.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Puchades, C. et al., Unique Structural Features of the Mitochondrial AAA+ Protease AFG3L2 Reveal the Molecular Basis for Activity in Health and Disease. Mol.Cell (2019)

Release Date

2019-05-22

Peptides

AFG3-like protein 2: ABCDEF
Substrate: GHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

AFG3-like protein 2

Substrate

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