SMTL ID : 6az0.1

Mitochondrial ATPase Protease YME1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: D.4, C.6, G.7, P.44, P.45, G.46, T.47, G.48, K.49, T.50, L.51, R.54, I.178, H.181, H.182, G.206, A.207 Chain B: D.131, R.157, R.160 Ligands: MG.3 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:C.6, A:C.6, A:G.46, A:T.47, A:G.48, A:K.49, A:T.50, A:L.51, A:G.206, A:A.207 Salt bridges: A:K.49, A:K.49, B:R.157, B:R.157, B:R.157, B:R.160 ATP.4: 21 residues within 4Å: Chain B: D.4, V.5, C.6, G.7, P.45, G.46, T.47, G.48, K.49, T.50, L.51, H.181, H.182, G.206, A.207, A.210 Chain C: D.131, Q.135, R.157, R.160 Ligands: MG.6 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:C.6, B:G.46, B:T.47, B:G.48, B:K.49, B:T.50, B:L.51, B:G.206 Salt bridges: B:K.49, B:K.49, C:R.157, C:R.157, C:R.157, C:R.160 ATP.7: 23 residues within 4Å: Chain C: D.4, V.5, C.6, G.7, P.45, G.46, T.47, G.48, K.49, T.50, L.51, R.54, Q.103, N.146, H.181, H.182, G.206, A.207, A.210 Chain D: D.131, R.157, R.160 Ligands: MG.9 17 PLIP interactions: 13 interactions with chain C, 4 interactions with chain D Hydrogen bonds: C:C.6, C:C.6, C:G.46, C:T.47, C:G.48, C:K.49, C:T.50, C:T.50, C:L.51, C:Q.103, C:N.146 Salt bridges: C:K.49, C:K.49, D:R.157, D:R.157, D:R.157, D:R.160 ATP.12: 22 residues within 4Å: Chain D: D.4, V.5, C.6, G.7, P.45, G.46, T.47, G.48, K.49, T.50, L.51, Q.103, N.146, H.181, H.182, G.206, A.207, A.210 Chain E: D.131, R.157, R.160 Ligands: MG.11 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain E Hydrogen bonds: D:C.6, D:G.7, D:G.46, D:T.47, D:G.48, D:K.49, D:T.50, D:T.50, D:L.51, D:Q.103, D:N.146, D:N.146 Salt bridges: D:K.49, D:K.49, E:R.157, E:R.157, E:R.157, E:R.160

6 x ZN: ZINC ION(Non-covalent)

ZN.2: 3 residues within 4Å: Chain A: H.262, H.266, D.340 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.262, A:H.266, A:D.340, A:D.340 ZN.5: 3 residues within 4Å: Chain B: H.262, H.266, D.340 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.262, B:H.266, B:D.340, B:D.340 ZN.8: 3 residues within 4Å: Chain C: H.262, H.266, D.340 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.262, C:H.266, C:D.340, C:D.340 ZN.10: 3 residues within 4Å: Chain D: H.262, H.266, D.340 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.262, D:H.266, D:D.340 ZN.14: 3 residues within 4Å: Chain E: H.262, H.266, D.340 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.262, E:H.266, E:D.340, E:D.340 ZN.15: 3 residues within 4Å: Chain F: H.262, H.266, D.340 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.262, F:H.266, F:D.340, F:D.340

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: T.50 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain B: T.50, D.102 Ligands: ATP.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.102 MG.9: 3 residues within 4Å: Chain C: T.50, D.102 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.50 MG.11: 4 residues within 4Å: Chain D: T.50, D.102 Chain E: D.131 Ligands: ATP.12 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.50

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

ADP.13: 16 residues within 4Å: Chain E: D.4, V.5, C.6, G.7, C.8, G.46, T.47, G.48, K.49, T.50, L.51, H.181, H.182, G.206, A.207, A.210 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:C.6, E:G.7, E:G.46, E:T.47, E:G.48, E:K.49, E:T.50, E:T.50, E:T.50, E:L.51 Salt bridges: E:K.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Puchades, C. et al., Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing. Science (2017)

Release Date

2017-11-15

Peptides

Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1: ABCDEF
poly(UNK): G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Mitochondrial inner membrane i-AAA protease supercomplex subunit YME1

poly(UNK)

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