SMTL ID : 5hwn.1

Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x PYR: PYRUVIC ACID(Covalent)(Non-covalent)

PYR.1: 10 residues within 4Å: Chain A: F.17, G.52, G.53, T.54, L.108, L.110, Y.140, K.166, G.191, S.211 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.17, A:K.166 Hydrogen bonds: A:G.53, A:T.54, A:T.54, A:Y.140 Water bridges: A:T.54 Salt bridges: A:K.166 PYR.8: 10 residues within 4Å: Chain B: F.17, G.52, G.53, T.54, L.108, L.110, Y.140, K.166, G.191, S.211 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.17, B:Y.140 Hydrogen bonds: B:G.53, B:T.54 PYR.13: 10 residues within 4Å: Chain C: F.17, G.52, G.53, T.54, L.108, L.110, Y.140, K.166, G.191, S.211 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.17, C:Y.140 Hydrogen bonds: C:G.53, C:T.54, C:T.54 Water bridges: C:T.54 PYR.16: 10 residues within 4Å: Chain D: F.17, G.52, G.53, T.54, L.108, L.110, Y.140, K.166, G.191, S.211 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.17 Hydrogen bonds: D:G.53, D:T.54, D:Y.140 Water bridges: D:T.54 Salt bridges: D:K.166

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: G.11, L.186, M.187, Y.188, L.189, G.206, F.207, T.208, T.209 Ligands: GOL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.188, A:Y.188, A:T.208, A:T.209 GOL.3: 9 residues within 4Å: Chain A: S.12, G.13, L.14, Y.43, K.44, A.45, P.46, N.223, Y.226 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.14 Water bridges: A:K.44, A:N.223 GOL.4: 10 residues within 4Å: Chain A: R.234, E.238 Chain D: R.176, T.179, A.180, G.183, D.184, Y.188, A.205, G.206 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:T.179, D:T.179, A:R.234, A:R.234, A:E.238 Water bridges: D:G.183, D:D.184 GOL.5: 11 residues within 4Å: Chain A: W.39, Y.43, F.217, V.218, P.219, G.220, L.221, Q.270, H.299, K.300, R.301 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.43, A:G.220, A:L.221, A:K.300 GOL.7: 6 residues within 4Å: Chain A: G.11, S.12, M.187, T.208, R.230 Ligands: GOL.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.11, A:R.230, A:R.230 Water bridges: A:G.11, A:G.11, A:T.208 GOL.9: 11 residues within 4Å: Chain B: W.39, Y.43, F.217, V.218, P.219, G.220, L.221, Q.270, H.299, K.300, R.301 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.43, B:G.220, B:L.221 GOL.10: 9 residues within 4Å: Chain B: G.11, L.186, M.187, Y.188, L.189, G.206, F.207, T.208, T.209 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.186, B:Y.188, B:T.208, B:T.209 Water bridges: B:T.208 GOL.11: 9 residues within 4Å: Chain B: R.234, E.238 Chain C: R.176, T.179, A.180, G.183, D.184, Y.188, G.206 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.234, B:R.234, C:R.176 GOL.14: 9 residues within 4Å: Chain C: G.11, L.186, M.187, Y.188, L.189, G.206, F.207, T.208, T.209 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.188, C:T.208, C:T.209 GOL.17: 8 residues within 4Å: Chain A: R.176, T.179, A.180, G.183, Y.188, G.206 Chain D: R.234, E.238 6 PLIP interactions: 1 interactions with chain A, 5 interactions with chain D Hydrogen bonds: A:T.179, D:R.234, D:R.234, D:E.238 Water bridges: D:E.238, D:E.238 GOL.18: 5 residues within 4Å: Chain D: G.11, M.187, T.208, R.230 Ligands: GOL.19 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.230, D:R.230 Water bridges: D:G.11 GOL.19: 10 residues within 4Å: Chain D: G.11, L.186, M.187, Y.188, L.189, G.206, F.207, T.208, T.209 Ligands: GOL.18 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.188, D:T.208, D:T.209

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 6 residues within 4Å: Chain A: G.53, F.58, Y.140, R.142, V.260 Chain B: I.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.142, A:R.142 Water bridges: A:R.142 FMT.12: 5 residues within 4Å: Chain A: I.115 Chain B: G.53, F.58, R.142, V.260 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.142, B:R.142 FMT.15: 5 residues within 4Å: Chain C: G.53, F.58, R.142, V.260 Chain D: I.115 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:D.116 Hydrogen bonds: C:R.142, C:R.142 FMT.20: 5 residues within 4Å: Chain C: I.115 Chain D: G.53, F.58, R.142, V.260 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.53, D:R.142, D:R.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taberman, H. et al., Structure and function of a decarboxylating Agrobacterium tumefaciens keto-deoxy-d-galactarate dehydratase. Biochemistry (2014)

Release Date

2016-03-23

Peptides

Probable 5-dehydro-4-deoxyglucarate dehydratase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Probable 5-dehydro-4-deoxyglucarate dehydratase

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