SMTL ID : 4hg5.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-dimer

Ligands

2 x OAA: OXALOACETATE ION(Non-covalent)

OAA.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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.165, A:Y.204 Hydrogen bonds: A:K.161, A:T.230 Salt bridges: A:R.207 OAA.6: 9 residues within 4Å: Chain B: K.161, F.165, C.203, Y.204, R.207, A.228, F.229, T.230, T.233 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.165, B:F.229 Hydrogen bonds: B:K.161, B:T.230, B:T.233 Salt bridges: B:R.207

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: K.70, L.312, I.313, L.314 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.70, A:K.70, A:L.314, A:L.314 GOL.3: 3 residues within 4Å: Chain A: R.41, K.70, L.314 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.41 Water bridges: A:R.41 GOL.4: 6 residues within 4Å: Chain A: K.197, R.216, G.219, A.220, E.221, R.326 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.197, A:R.216, A:R.326 GOL.5: 2 residues within 4Å: Chain A: D.189, I.190 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.189, A:I.190 GOL.7: 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, A:G.297

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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