SMTL ID : 5kc1.1 (2 other biounits)

Structure of the C-terminal dimerization domain of Atg38

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: L.138, N.141 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.141, B:E.173 NA.5: 1 residues within 4Å: Chain B: E.168 No protein-ligand interaction detected (PLIP) NA.6: 2 residues within 4Å: Chain B: K.162 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.162, B:K.162 NA.15: 4 residues within 4Å: Chain A: Q.139 Chain D: E.168, K.171 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.168, D:K.171

6 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 4 residues within 4Å: Chain A: L.130, S.133, I.134, R.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.137 NO3.7: 6 residues within 4Å: Chain B: M.161, K.162, I.163, N.164, L.165, R.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.165, B:R.166 NO3.8: 1 residues within 4Å: Chain B: R.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.166, B:R.166 NO3.11: 4 residues within 4Å: Chain C: N.136, Q.139, F.140, N.143 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.164, C:Q.139, C:N.143 Water bridges: B:N.164 NO3.12: 4 residues within 4Å: Chain B: K.171 Chain C: M.132, N.136, Q.139 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.171, C:Q.139 NO3.16: 6 residues within 4Å: Chain C: I.134, R.137 Chain D: R.166, Q.169, F.170, E.173 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:R.166, C:R.137, C:R.137 Water bridges: D:R.166

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: I.126, P.129, M.132 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.126 EDO.4: 4 residues within 4Å: Chain A: M.132, N.136 Chain D: K.171 Ligands: NA.15 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:K.171, A:M.132 EDO.13: 1 residues within 4Å: Chain C: N.127 No protein-ligand interaction detected (PLIP) EDO.14: 3 residues within 4Å: Chain B: K.162 Chain C: Q.147 Ligands: NA.6 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.162, C:Q.147

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 1 residues within 4Å: Chain B: Q.169 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain B: K.172, V.175, L.176 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohashi, Y. et al., Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex. Autophagy (2016)

Release Date

2016-10-05

Peptides

Autophagy-related protein 38: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
A

D
B

Autophagy-related protein 38

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