SMTL ID : 4gel.1

Crystal structure of Zucchini

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.30, H.34, C.50, C.55 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.30, A:H.34, A:C.50, A:C.55 ZN.5: 4 residues within 4Å: Chain B: C.30, H.34, C.50, C.55 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.30, B:H.34, B:C.50, B:C.55

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 2 residues within 4Å: Chain A: K.112, G.113 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.113, A:S.114 Salt bridges: A:K.112

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

EDO.3: 5 residues within 4Å: Chain A: G.106, E.107, P.129, I.130, T.131 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.131 EDO.4: 6 residues within 4Å: Chain A: P.129, I.130, A.208, F.209 Chain B: E.25, W.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.130 Water bridges: A:I.130 EDO.6: 5 residues within 4Å: Chain B: D.143, F.145, C.163, Y.164, S.165 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.143, B:S.165 EDO.7: 5 residues within 4Å: Chain B: N.24, E.25, G.27, E.28, G.181 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Water bridges: A:N.133, B:G.181, B:G.181 Hydrogen bonds: B:G.27, B:E.28 EDO.8: 6 residues within 4Å: Chain B: R.69, V.71, D.143, C.163, Y.164, I.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.69, B:R.69, B:D.143, B:D.143, B:Y.164 EDO.9: 6 residues within 4Å: Chain B: L.94, V.98, I.99, I.100, G.123, P.125 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishimasu, H. et al., Structure and function of Zucchini endoribonuclease in piRNA biogenesis. Nature (2012)

Release Date

2012-10-17

Peptides

Mitochondrial cardiolipin hydrolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Mitochondrial cardiolipin hydrolase