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

Structure of the C-terminal dimerization domain of Atg38

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

NO3.1: 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 NO3.2: 1 residues within 4Å: Chain A: F.140 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.144 NO3.3: 3 residues within 4Å: Chain A: F.140, N.144, Q.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.144 Water bridges: A:N.143 NO3.4: 2 residues within 4Å: Chain A: Q.147, E.151 No protein-ligand interaction detected (PLIP) NO3.5: 5 residues within 4Å: Chain A: K.149 Chain B: K.162, I.163, L.165, R.166 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.149, B:L.165, B:R.166 NO3.14: 4 residues within 4Å: Chain C: R.137 Chain D: R.166, F.170, E.173 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.166, D:E.173, C:R.137

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

NA.6: 3 residues within 4Å: Chain C: D.128, P.129 Ligands: CL.7 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.128, C:L.130 NA.10: 3 residues within 4Å: Chain D: Q.169, K.172, E.173 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.169, D:E.173 NA.11: 1 residues within 4Å: Chain D: E.168 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.168 NA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NA.13: 4 residues within 4Å: Chain D: K.172, V.175, L.176 Ligands: CL.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.172

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

CL.7: 1 residues within 4Å: Ligands: NA.6 Ligand excluded by PLIP CL.8: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.15: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.16: 1 residues within 4Å: Ligands: NA.13 Ligand excluded by PLIP

1 x IOD: IODIDE ION(Non-functional Binders)

IOD.9: 3 residues within 4Å: Chain C: Q.139, F.140, N.143 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
G

B
H

C
E

D
F

Autophagy-related protein 38

Related Entries With Identical Sequence