SMTL ID : 6dka.1 (4 other biounits)

Yeast Ddi2 Cyanamide Hydratase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.63, H.96, D.97, V.165, N.169, W.194 Ligands: CNN.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.63, A:H.96, A:D.97 ZN.6: 7 residues within 4Å: Chain B: H.63, H.96, D.97, V.165, N.169, W.194 Ligands: CNN.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.63, B:H.96, B:D.97

2 x CNN: CYANAMIDE(Non-covalent)

CNN.2: 10 residues within 4Å: Chain A: H.63, H.96, D.97, F.112, H.145, Q.146, V.165, N.169, F.198 Ligands: ZN.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.96, A:H.145, A:N.169 CNN.7: 10 residues within 4Å: Chain B: H.63, H.96, D.97, F.112, H.145, Q.146, V.165, N.169, F.198 Ligands: ZN.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.96, B:H.145, B:N.169

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 4 residues within 4Å: Chain A: H.193, L.195, S.196 Ligands: SO4.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.195, A:S.196, A:S.196, A:S.196 Salt bridges: A:H.193 SO4.4: 5 residues within 4Å: Chain A: R.191, H.193, W.194, L.195 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.194, A:L.195 Salt bridges: A:R.191 SO4.5: 2 residues within 4Å: Chain A: R.106, R.208 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.106, A:R.208 SO4.8: 4 residues within 4Å: Chain B: H.193, L.195, S.196 Ligands: SO4.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.195, B:S.196, B:S.196, B:S.196 Salt bridges: B:H.193 SO4.9: 5 residues within 4Å: Chain B: R.191, H.193, W.194, L.195 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.194, B:L.195 Salt bridges: B:R.191 SO4.10: 2 residues within 4Å: Chain B: R.106, R.208 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.106, B:R.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, J. et al., Structure of Ddi2, a highly inducible detoxifying metalloenzyme fromSaccharomyces cerevisiae. J.Biol.Chem. (2019)

Release Date

2019-05-08

Peptides

DNA damage-inducible protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA damage-inducible protein

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