SMTL ID : 5yec.1

Crystal structure of Atg7CTD-Atg8-MgATP complex in form II

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.195, C.198, C.279, C.282 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.195, A:C.198, A:C.279, A:C.282 ZN.4: 4 residues within 4Å: Chain C: C.195, C.198, C.279, C.282 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.195, C:C.198, C:C.279, C:C.282

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

ATP.2: 18 residues within 4Å: Chain A: G.41, A.42, G.43, T.44, D.65, N.66, G.67, N.73, Q.77, K.89, L.111, S.112, I.113, M.115, V.147, D.148, S.152 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.44, A:T.44, A:N.66, A:G.67, A:N.73, A:Q.77, A:K.89, A:I.113, A:I.113, A:D.148, A:S.152 Water bridges: A:L.45, A:M.115 Salt bridges: A:K.89, A:K.89 ATP.5: 17 residues within 4Å: Chain C: G.41, A.42, G.43, T.44, D.65, N.66, G.67, N.73, Q.77, K.89, L.111, S.112, I.113, M.115, D.148, S.152 Ligands: MG.6 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.44, C:N.66, C:N.73, C:Q.77, C:I.113, C:I.113, C:S.152 Water bridges: C:L.45, C:S.70, C:N.73, C:N.73, C:K.89 Salt bridges: C:K.89, C:K.89

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: D.148 Ligands: ATP.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.148 MG.6: 2 residues within 4Å: Chain C: D.148 Ligands: ATP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamaguchi, M. et al., Atg7 Activates an Autophagy-Essential Ubiquitin-like Protein Atg8 through Multi-Step Recognition. J. Mol. Biol. (2018)

Release Date

2018-03-28

Peptides

Ubiquitin-like modifier-activating enzyme ATG7: AC
Autophagy-related protein 8: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Ubiquitin-like modifier-activating enzyme ATG7

Autophagy-related protein 8

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