SMTL ID : 4hg3.2 (1 other biounit)

Structural insights into yeast Nit2: wild-type yeast Nit2 in complex with alpha-ketoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

homo-dimer

Ligands

2 x AKG: 2-OXOGLUTARIC ACID(Covalent)

AKG.1: 10 residues within 4Å: Chain A: E.79, K.161, F.165, C.203, Y.204, R.207, A.228, F.229, T.230, T.233 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.165, A:F.165, A:F.229 Hydrogen bonds: A:K.161, A:Y.204, A:T.230 Water bridges: A:A.228 Salt bridges: A:R.207 AKG.9: 10 residues within 4Å: Chain B: E.79, K.161, F.165, C.203, Y.204, R.207, A.228, F.229, T.230, T.233 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.165, B:F.165, B:F.229 Hydrogen bonds: B:K.161, B:Y.204, B:T.230 Water bridges: B:A.228 Salt bridges: B:R.207

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.216, R.326, N.327, P.330, N.333 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.216, A:N.327 Water bridges: A:M.329 GOL.3: 3 residues within 4Å: Chain A: K.70, L.312, L.314 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.70, A:K.70 Water bridges: A:L.314 GOL.4: 5 residues within 4Å: Chain A: K.197, G.219, A.220, R.326 Ligands: GOL.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.197, A:R.216, A:R.326 Water bridges: A:R.216, A:R.216 GOL.5: 6 residues within 4Å: Chain A: R.243, W.296, G.297, K.298 Chain B: A.236, H.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.243, A:W.296 Water bridges: A:R.243 GOL.6: 4 residues within 4Å: Chain A: Y.93, K.97, D.266, E.268 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.93, A:K.97, A:D.266 Water bridges: A:E.268 GOL.10: 6 residues within 4Å: Chain A: A.236, H.237 Chain B: R.243, W.296, G.297, K.298 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.243, A:H.237 GOL.11: 7 residues within 4Å: Chain B: P.173, T.230, I.231, K.232, R.283, R.284, E.285 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.231, B:K.232, B:R.283, B:E.285, B:E.285

3 x CAC: CACODYLATE ION(Non-covalent)

CAC.7: 4 residues within 4Å: Chain A: P.99, I.102, L.128, E.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.158 CAC.8: 7 residues within 4Å: Chain A: E.79, L.84, H.127, N.144, E.177, V.181, R.284 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.284, A:R.284 Water bridges: A:S.85 CAC.12: 8 residues within 4Å: Chain B: E.79, A.80, L.84, H.127, N.144, E.177, V.181, R.284 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.284, B:R.284

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., Structures of enzyme-intermediate complexes of yeast Nit2: insights into its catalytic mechanism and different substrate specificity compared with mammalian Nit2. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-07-31

Peptides

Probable hydrolase NIT2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Probable hydrolase NIT2

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