SMTL ID : 4hg3.1 (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 10 PLIP interactions: 10 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, A:T.233, A:T.233 Water bridges: A:A.228 Salt bridges: A:R.207 AKG.11: 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 9 PLIP interactions: 9 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, B:T.233, B:T.233 Salt bridges: B:R.207

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 2 residues within 4Å: Chain A: R.92, Y.93 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.96, A:D.140 GOL.3: 2 residues within 4Å: Chain A: H.151, P.194 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.151 GOL.4: 3 residues within 4Å: Chain A: D.189, I.190, M.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.189, A:D.189, A:I.190 Water bridges: A:M.218 GOL.5: 4 residues within 4Å: Chain A: R.326, N.327, P.330, N.333 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.326, A:N.327 Water bridges: A:Q.250, A:N.333, A:N.333 GOL.6: 1 residues within 4Å: Chain A: I.300 No protein-ligand interaction detected (PLIP) GOL.7: 6 residues within 4Å: Chain A: R.243, W.296, G.297, K.298 Chain B: A.236, H.237 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.237, A:R.243 GOL.8: 4 residues within 4Å: Chain A: Y.93, K.97, D.266, E.268 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.97, A:K.97, A:D.266 Water bridges: A:D.266, A:E.268 GOL.12: 2 residues within 4Å: Chain B: S.107, T.110 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.110 Water bridges: B:S.107, B:S.107 GOL.13: 4 residues within 4Å: Chain B: C.48, G.260, M.261, V.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:M.261, B:M.261

4 x CAC: CACODYLATE ION(Non-covalent)

CAC.9: 4 residues within 4Å: Chain A: I.102, L.128, I.155, E.158 No protein-ligand interaction detected (PLIP) CAC.10: 7 residues within 4Å: Chain A: E.79, A.80, L.84, H.127, E.177, V.181, R.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.284, A:R.284 CAC.14: 6 residues within 4Å: Chain B: S.85, N.87, P.88, S.180, R.284 Ligands: CAC.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.85, B:R.284 Water bridges: B:S.85, B:S.85 CAC.15: 8 residues within 4Å: Chain B: E.79, L.84, H.127, N.144, E.177, V.181, R.284 Ligands: CAC.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.144 Water bridges: B:K.161

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
A

B
C

Probable hydrolase NIT2

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