SMTL ID : 4hgd.1 (1 other biounit)

Structural insights into yeast Nit2: C169S mutant of yeast Nit2 in complex with an endogenous peptide-like ligand

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 2 residues within 4Å: Chain A: R.92, Y.93 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Y.93, A:Y.93 GOL.2: 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:I.190, A:I.190 Water bridges: A:M.218 GOL.3: 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.4: 4 residues within 4Å: Chain A: G.219, A.220, E.221, R.326 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.216, A:R.326 GOL.5: 6 residues within 4Å: Chain A: P.173, T.230, I.231, K.232, R.284, E.285 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.230, A:I.231, A:K.232, A:E.285 GOL.8: 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:G.297 GOL.9: 8 residues within 4Å: Chain B: E.158, Y.159, Q.160, L.162, G.184, K.185, A.186, P.188 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.158, B:Q.160, B:K.185, B:A.186 GOL.10: 4 residues within 4Å: Chain B: S.217, W.332, R.335, D.337 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.217, B:W.332

2 x CAC: CACODYLATE ION(Non-covalent)

CAC.6: 4 residues within 4Å: Chain A: P.99, I.102, I.155, E.158 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.106 CAC.11: 3 residues within 4Å: Chain B: R.216, R.326, W.332 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.216, B:R.326

2 x KGT: N-(4-carboxy-4-oxobutanoyl)-L-cysteinylglycine(Non-covalent)

KGT.7: 14 residues within 4Å: Chain A: E.79, L.84, H.127, K.161, F.165, E.177, S.203, Y.204, R.207, A.228, F.229, T.230, T.233, R.284 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.165, A:F.229 Hydrogen bonds: A:K.161, A:S.203, A:Y.204, A:A.228, A:T.230, A:R.284, A:R.284 Salt bridges: A:H.127, A:R.207, A:R.284 KGT.12: 15 residues within 4Å: Chain B: E.79, L.84, H.127, N.144, K.161, F.165, E.177, S.203, Y.204, R.207, A.228, F.229, T.230, T.233, R.284 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.165, B:F.229 Hydrogen bonds: B:N.144, B:K.161, B:E.177, B:S.203, B:A.228, B:T.230, B:T.233, B:R.284, B:R.284 Salt bridges: B:H.127, B:R.207, 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
A

B
D

Probable hydrolase NIT2

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