SMTL ID : 6dkc.2 (4 other biounits)

Yeast Ddi2 Cyanamide Hydratase, T157V mutant, apo structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 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 SO4.3: 4 residues within 4Å: Chain A: H.193, L.195, S.196 Ligands: SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.195, A:S.196 Salt bridges: A:H.193 SO4.4: 6 residues within 4Å: Chain A: R.191, H.193, W.194, L.195, S.196 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: 3 residues within 4Å: Chain A: P.33, R.34, A.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.35 SO4.6: 5 residues within 4Å: Chain A: V.37, P.38, V.72, R.76, Q.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.86, A:Q.86 Salt bridges: A:R.76 SO4.8: 6 residues within 4Å: Chain B: R.191, H.193, W.194, L.195, S.196 Ligands: SO4.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.194, B:L.195 Salt bridges: B:R.191 SO4.9: 5 residues within 4Å: Chain B: H.193, W.194, L.195, S.196 Ligands: SO4.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.195, B:S.196 Salt bridges: B:H.193 SO4.10: 4 residues within 4Å: Chain B: R.32, R.34, A.35, V.37 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.32, B:A.35 Water bridges: B:R.76 SO4.11: 6 residues within 4Å: Chain B: V.72, I.75, R.76, L.84, Q.86, L.89 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.84, B:Q.86 Salt bridges: B:R.76 SO4.12: 4 residues within 4Å: Chain B: V.37, P.38, R.76, Q.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.86 Water bridges: B:R.76 Salt bridges: B:R.76 SO4.13: 3 residues within 4Å: Chain B: R.32, R.34, R.76 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.32, B:R.34

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.63, H.96, D.97, V.165, N.169, W.194 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.63, A:H.96, A:D.97, H2O.1 ZN.7: 6 residues within 4Å: Chain B: H.63, H.96, D.97, V.165, N.169, W.194 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.63, B:H.96, B:D.97, H2O.2

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
B

B
C

DNA damage-inducible protein

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