SMTL ID : 2yy7.1

Crystal structure of thermolabile L-threonine dehydrogenase from Flavobacterium frigidimaris KUC-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

4 x PE8: 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL(Non-covalent)

PE8.1: 5 residues within 4Å: Chain A: T.82, E.84, K.85, F.271, R.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.85 PE8.2: 10 residues within 4Å: Chain A: F.99, N.103, K.106, A.107, W.153, Y.157, Y.161 Chain B: P.87, A.88, W.91 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.103, A:K.106 Water bridges: A:Y.157, A:Y.157 PE8.6: 6 residues within 4Å: Chain B: A.81, T.82, E.84, K.85, F.271, R.272 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.85 Water bridges: B:R.272 PE8.7: 13 residues within 4Å: Chain A: P.87, A.88, W.91 Chain B: L.55, N.96, F.99, H.100, N.103, K.106, A.107, W.153, Y.157, Y.161 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.103, B:K.106, B:Y.157 Water bridges: B:L.55, B:F.57

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.3: 27 residues within 4Å: Chain A: G.9, C.11, G.12, Q.13, I.14, D.35, I.36, R.37, V.52, N.53, A.54, M.75, A.76, A.77, L.79, L.93, P.116, S.117, S.118, Y.143, K.147, Y.170, P.171, G.172, L.173, G.181 Ligands: GOL.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:Y.170 Hydrogen bonds: A:C.11, A:C.11, A:Q.13, A:Q.13, A:I.14, A:I.36, A:R.37, A:R.37, A:N.53, A:A.54, A:M.75, A:K.147, A:L.173 Water bridges: A:G.12, A:G.15, A:P.180, A:G.181, A:G.181 pi-Stacking: A:Y.170 NAD.8: 27 residues within 4Å: Chain B: G.9, C.11, G.12, Q.13, I.14, D.35, I.36, R.37, V.52, N.53, A.54, M.75, A.76, A.77, L.79, L.93, P.116, S.117, S.118, Y.143, K.147, Y.170, P.171, G.172, L.173, G.181 Ligands: GOL.10 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.170 Hydrogen bonds: B:C.11, B:C.11, B:Q.13, B:Q.13, B:I.14, B:G.15, B:I.36, B:R.37, B:R.37, B:N.53, B:A.54, B:M.75, B:Y.143, B:K.147, B:L.173 Water bridges: B:G.12, B:G.12, B:P.180, B:G.181, B:G.181, B:T.185 pi-Stacking: B:Y.170

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.4: 6 residues within 4Å: Chain A: E.202, C.203, F.204, E.268, D.270, R.272 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.272 MES.9: 6 residues within 4Å: Chain B: E.202, C.203, F.204, E.268, D.270, R.272 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.272 Salt bridges: B:E.268

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: S.80, S.118, I.119, Y.143, G.183, T.184, T.185, W.279 Ligands: NAD.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.80, A:S.118, A:Y.143, A:Y.143, A:T.184, A:T.185 Water bridges: A:G.183 GOL.10: 9 residues within 4Å: Chain B: S.80, S.118, I.119, Y.143, G.183, T.184, T.185, W.279 Ligands: NAD.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.80, B:S.80, B:S.118, B:Y.143, B:T.184, B:T.185 Water bridges: B:G.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoneda, K. et al., Crystal structure of UDP-galactose 4-epimerase-like L-threonine dehydrogenase belonging to the intermediate short-chain dehydrogenase-reductase superfamily. Febs J. (2010)

Release Date

2008-04-29

Peptides

L-threonine dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

L-threonine dehydrogenase