SMTL ID : 1w3i.1

Sulfolobus solfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with pyruvate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x PYR: PYRUVIC ACID(Covalent)

PYR.1: 8 residues within 4Å: Chain A: P.6, F.38, G.41, T.42, T.43, Y.129, K.154, V.195 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.6, A:P.6, A:K.154, A:V.195 Hydrogen bonds: A:T.42, A:T.43, A:T.43, A:Y.129 Salt bridges: A:K.154 PYR.4: 8 residues within 4Å: Chain B: P.6, F.38, G.41, T.42, T.43, Y.129, K.154, V.195 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.6, B:P.6, B:K.154, B:V.195 Hydrogen bonds: B:T.42, B:T.43 Water bridges: B:Y.129 Salt bridges: B:K.154 PYR.7: 10 residues within 4Å: Chain C: P.6, F.38, G.41, T.42, T.43, Y.129, K.154, G.178, V.195 Ligands: GOL.8 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:P.6, C:P.6, C:K.154, C:V.195 Hydrogen bonds: C:T.42, C:T.43, C:T.43 Water bridges: C:Y.129 Salt bridges: C:K.154 PYR.12: 10 residues within 4Å: Chain D: P.6, F.38, G.41, T.42, T.43, Y.129, K.154, G.178, V.195 Ligands: GOL.13 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:P.6, D:P.6, D:K.154, D:V.195 Hydrogen bonds: D:T.42, D:T.42, D:T.43, D:T.43, D:Y.129 Salt bridges: D:K.154

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: G.239, S.240, L.241, S.242, I.263 Chain D: R.105, M.106, S.107, H.110 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:S.240, A:L.241, A:S.242, A:S.242, D:S.107, D:S.107 Water bridges: A:S.240 GOL.3: 5 residues within 4Å: Chain A: C.119, H.124, P.125, V.126, C.149 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.149 Water bridges: A:S.122 GOL.5: 10 residues within 4Å: Chain B: F.238, G.239, S.240, L.241, S.242, I.263 Chain C: R.105, M.106, S.107, H.110 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B Hydrogen bonds: C:S.107, C:S.107, B:S.240, B:S.240, B:L.241, B:S.242, B:S.242 GOL.6: 4 residues within 4Å: Chain B: H.124, P.125, V.126, C.149 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.119, B:C.149 Water bridges: B:V.126 GOL.8: 7 residues within 4Å: Chain C: T.42, T.43, Y.131, T.156, A.197, L.241 Ligands: PYR.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.43 Water bridges: C:S.240, C:N.244 GOL.9: 9 residues within 4Å: Chain B: R.105, M.106, S.107, H.110 Chain C: G.239, S.240, L.241, S.242, I.263 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:S.240, C:L.241, C:S.242, C:S.242, B:S.107, B:S.107 Water bridges: C:S.240 GOL.10: 4 residues within 4Å: Chain C: I.92, P.123, H.124, P.125 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.124 GOL.11: 6 residues within 4Å: Chain C: C.119, S.122, H.124, P.125, V.126, C.149 4 PLIP interactions: 4 interactions with chain C Water bridges: C:C.119, C:S.122, C:C.149, C:T.151 GOL.13: 7 residues within 4Å: Chain D: T.42, T.43, Y.131, T.156, A.197, L.241 Ligands: PYR.12 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.43, D:Y.131, D:Y.131 Water bridges: D:S.240, D:N.244 GOL.14: 10 residues within 4Å: Chain A: R.105, M.106, S.107, H.110 Chain D: F.238, G.239, S.240, L.241, S.242, I.263 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:R.105, A:S.107, A:S.107, D:L.241, D:S.242, D:S.242 Water bridges: D:S.240

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