SMTL ID : 1w3t.1

Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDGal, D-Glyceraldehyde and pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x RSH: 3-DEOXY-D-LYXO-HEXONIC ACID(Covalent)

RSH.1: 12 residues within 4Å: Chain A: P.7, F.39, G.42, T.43, T.44, Y.130, Y.132, K.155, T.157, A.198 Ligands: PYR.2, 3GR.3 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:P.7, A:K.155 Hydrogen bonds: A:T.43, A:T.43, A:T.44, A:Y.130, A:K.155, A:K.155, A:T.157 Salt bridges: A:K.155 RSH.5: 11 residues within 4Å: Chain B: P.7, F.39, G.42, T.43, T.44, Y.130, Y.132, K.155, T.157 Ligands: PYR.6, 3GR.7 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:P.7, B:K.155 Hydrogen bonds: B:T.43, B:T.44, B:Y.130, B:Y.130, B:Y.132, B:T.157 Salt bridges: B:K.155 RSH.9: 13 residues within 4Å: Chain C: P.7, F.39, G.42, T.43, T.44, Y.130, Y.132, K.155, T.157, A.198, L.242 Ligands: PYR.10, 3GR.11 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:P.7, C:K.155 Hydrogen bonds: C:T.43, C:T.44, C:T.44, C:T.44, C:Y.130, C:K.155 Salt bridges: C:K.155 RSH.13: 12 residues within 4Å: Chain D: P.7, F.39, G.42, T.43, T.44, Y.130, Y.132, K.155, T.157, G.179 Ligands: PYR.14, 3GR.15 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:P.7, D:K.155 Hydrogen bonds: D:T.43, D:T.44, D:T.44, D:Y.130, D:Y.130, D:Y.132 Water bridges: D:S.241 Salt bridges: D:K.155

4 x PYR: PYRUVIC ACID(Covalent)

PYR.2: 10 residues within 4Å: Chain A: P.7, F.39, G.42, T.43, T.44, Y.130, K.155, V.196 Ligands: RSH.1, 3GR.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:P.7, A:K.155 Hydrogen bonds: A:T.43, A:T.44, A:Y.130 Salt bridges: A:K.155 PYR.6: 11 residues within 4Å: Chain B: P.7, F.39, G.42, T.43, T.44, Y.130, K.155, G.179, V.196 Ligands: RSH.5, 3GR.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.7, B:P.7, B:K.155, B:V.196 Hydrogen bonds: B:T.43, B:T.44 Salt bridges: B:K.155 PYR.10: 10 residues within 4Å: Chain C: P.7, F.39, G.42, T.43, T.44, Y.130, K.155, V.196 Ligands: RSH.9, 3GR.11 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:P.7, C:P.7, C:K.155, C:V.196 Hydrogen bonds: C:T.43, C:T.44, C:T.44 Salt bridges: C:K.155 PYR.14: 10 residues within 4Å: Chain D: P.7, F.39, G.42, T.43, T.44, Y.130, K.155, V.196 Ligands: RSH.13, 3GR.15 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:P.7, D:P.7, D:K.155 Hydrogen bonds: D:T.43, D:T.43, D:T.44, D:T.44, D:Y.130 Salt bridges: D:K.155

4 x 3GR: D-Glyceraldehyde(Non-covalent)

3GR.3: 11 residues within 4Å: Chain A: T.43, T.44, Y.130, Y.132, K.155, T.157, G.179, A.198, L.242 Ligands: RSH.1, PYR.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.132, A:K.155, A:T.157 3GR.7: 8 residues within 4Å: Chain B: T.43, Y.130, Y.132, K.155, T.157, G.179 Ligands: RSH.5, PYR.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.130, B:T.157, B:T.157 Water bridges: B:T.44, B:G.179, B:D.181, B:D.181 3GR.11: 10 residues within 4Å: Chain C: T.43, T.44, Y.130, Y.132, K.155, T.157, A.198, L.242 Ligands: RSH.9, PYR.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.130 3GR.15: 8 residues within 4Å: Chain D: T.43, Y.130, Y.132, K.155, T.157, G.179 Ligands: RSH.13, PYR.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.132, D:T.157 Water bridges: D:D.181

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: G.240, S.241, L.242, S.243, I.264 Chain D: R.106, M.107, S.108, H.111 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.241, A:S.241, A:L.242, A:S.243, A:S.243, D:S.108, D:S.108 GOL.8: 8 residues within 4Å: Chain B: G.240, S.241, L.242, S.243 Chain C: R.106, M.107, S.108, H.111 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:S.241, B:S.241, B:L.242, B:S.243, B:S.243, C:S.108, C:S.108 Water bridges: B:F.265 GOL.12: 10 residues within 4Å: Chain B: R.106, M.107, S.108, H.111 Chain C: F.239, G.240, S.241, L.242, S.243, I.264 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.241, C:S.241, C:L.242, C:S.243, C:S.243, B:S.108, B:S.108 Water bridges: C:F.265 GOL.16: 9 residues within 4Å: Chain A: R.106, M.107, H.111 Chain D: G.240, S.241, L.242, S.243, P.263, I.264 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.240, D:L.242, D:S.243, D:P.263, D:F.265 Water bridges: D:S.241, D:S.241

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Theodossis, A. et al., The structural basis for substrate promiscuity in 2-keto-3-deoxygluconate aldolase from the Entner-Doudoroff pathway in Sulfolobus solfataricus. J. Biol. Chem. (2004)

Release Date

2004-09-02

Peptides

2-KETO-3-DEOXY GLUCONATE ALDOLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

2-KETO-3-DEOXY GLUCONATE ALDOLASE

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