SMTL ID : 4h5u.2 (1 other biounit)

Structural insights into yeast Nit2: wild-type yeast Nit2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

homo-dimer

Ligands

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: D.189, I.190, M.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.190, A:I.190 Water bridges: A:M.218 GOL.2: 6 residues within 4Å: Chain A: R.216, R.326, N.327, P.330, N.333 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.216, A:N.327, A:N.333 Water bridges: A:M.329 GOL.3: 7 residues within 4Å: Chain A: K.197, R.216, G.219, A.220, E.221, R.326 Ligands: GOL.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.216, A:G.219, A:R.326 Water bridges: A:K.197, A:K.197 GOL.4: 6 residues within 4Å: Chain A: R.243, W.296, G.297, K.298 Chain B: A.236, H.237 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.243, B:H.237 Water bridges: A:I.299 GOL.6: 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 GOL.7: 6 residues within 4Å: Chain A: A.236, H.237 Chain B: R.243, W.296, G.297, K.298 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.243, B:W.296 Water bridges: B:R.243, B:W.296 GOL.8: 8 residues within 4Å: Chain B: R.216, Q.250, R.326, M.329, P.330, L.331, W.332, N.333 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.216, B:R.216, B:W.332

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.5: 4 residues within 4Å: Chain A: P.99, I.102, L.128, E.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.158 Water bridges: A:R.143

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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