SMTL ID : 5xpc.1

Crystal Structure of Drep4 CIDE domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-pentamer

Ligands

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: Y.23, K.40 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.23 GOL.2: 5 residues within 4Å: Chain A: L.50, S.52, P.67 Chain B: K.13, Q.69 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.13, B:K.13, A:S.52 GOL.3: 7 residues within 4Å: Chain A: H.47, E.56, P.77, D.78 Chain B: Y.23, K.40 Ligands: GOL.4 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.23, A:D.78 GOL.4: 8 residues within 4Å: Chain A: Y.49, G.54, E.56, A.79 Chain B: T.20, R.21, K.22 Ligands: GOL.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.20, B:K.22, A:E.56, A:E.56 GOL.5: 6 residues within 4Å: Chain B: L.50, S.52, L.66, P.67 Chain C: K.13, Q.69 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.52, C:K.13, C:K.13 GOL.6: 5 residues within 4Å: Chain C: S.52, D.53, T.70 Chain D: K.13 Ligands: GOL.8 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:S.52, D:K.13, D:K.13 Water bridges: C:T.70, C:L.71 GOL.7: 3 residues within 4Å: Chain C: D.59, E.61 Chain D: K.36 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:K.36, C:D.59, C:D.59, C:E.61 Water bridges: C:D.60 GOL.8: 6 residues within 4Å: Chain C: L.50, L.66, P.67 Chain D: K.13, Q.69 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.13, D:K.13 GOL.9: 8 residues within 4Å: Chain D: H.47, Y.49, E.56, P.77, D.78 Chain E: Y.23, K.40 Ligands: GOL.10 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:Y.23, E:K.40, D:Y.49, D:Y.49, D:D.78 GOL.10: 7 residues within 4Å: Chain D: Y.49, E.56, D.78 Chain E: R.21, K.22, Y.23 Ligands: GOL.9 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:K.22, E:K.22, D:Y.49, D:D.78 GOL.11: 5 residues within 4Å: Chain D: L.50, L.66, P.67 Chain E: K.13, Q.69 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:D.53, E:K.13 GOL.12: 3 residues within 4Å: Chain E: L.50, L.66, P.67 2 PLIP interactions: 2 interactions with chain E Water bridges: E:S.52, E:S.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, J.Y. et al., CIDE domains form functionally important higher-order assemblies for DNA fragmentation. Proc. Natl. Acad. Sci. U.S.A. (2017)

Release Date

2017-07-26

Peptides

DNAation factor-related protein 4: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

DNAation factor-related protein 4

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