SMTL ID : 6g3z.1

Sulfolobus sulfataricus 2-keto-3-deoxygluconate (KDG) aldolase complex with D-KDPG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-tetramer

Ligands

4 x ELE: 2-keto 3 deoxy 6 phospho gluconate(Covalent)

ELE.1: 17 residues within 4Å: Chain A: P.7, F.39, G.42, T.43, T.44, Y.130, Y.132, K.155, T.157, G.179, V.196, A.198, R.237, S.241, L.242 Chain D: P.105, R.106 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:P.7, A:K.155 Hydrogen bonds: A:T.43, A:T.44, A:T.44, A:Y.130, A:Y.132, A:T.157, A:T.157, A:S.241 Water bridges: A:T.44, A:A.198, A:R.237, A:R.237, A:S.241 Salt bridges: A:K.155, D:R.106 ELE.7: 16 residues within 4Å: Chain B: P.7, F.39, G.42, T.43, T.44, Y.130, Y.132, K.155, T.157, G.179, V.196, A.198, S.241, L.242 Chain C: P.105, R.106 19 PLIP interactions: 18 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:P.7, B:K.155 Hydrogen bonds: B:T.43, B:T.44, B:T.44, B:Y.130, B:Y.132, B:T.157, B:T.157, B:S.241, B:S.241 Water bridges: B:T.44, B:D.181, B:D.181, B:R.237, B:S.241, B:S.241 Salt bridges: B:K.155, C:R.106 ELE.10: 17 residues within 4Å: Chain B: P.105, R.106 Chain C: P.7, F.39, G.42, T.43, T.44, Y.130, Y.132, K.155, T.157, G.179, V.196, A.198, R.237, S.241, L.242 18 PLIP interactions: 17 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:P.7, C:K.155 Hydrogen bonds: C:T.43, C:T.44, C:T.44, C:Y.130, C:Y.132, C:T.157, C:T.157, C:S.241 Water bridges: C:T.44, C:D.181, C:A.198, C:R.237, C:R.237, C:S.241 Salt bridges: C:K.155, B:R.106 ELE.16: 16 residues within 4Å: Chain A: P.105, R.106 Chain D: P.7, F.39, G.42, T.43, T.44, Y.130, Y.132, K.155, T.157, G.179, V.196, A.198, S.241, L.242 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:P.7, D:K.155 Hydrogen bonds: D:T.43, D:T.44, D:T.44, D:Y.130, D:Y.132, D:T.157, D:T.157, D:S.241, D:S.241 Water bridges: D:T.44, D:D.181, D:D.181, D:D.181, D:R.237, D:S.241, D:S.241 Salt bridges: D:K.155, A:R.106

14 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.2: 4 residues within 4Å: Chain A: K.114, K.117, T.118, E.121 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.114 IPA.3: 6 residues within 4Å: Chain A: D.220, L.223, K.224, F.227 Chain B: K.168, P.172 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.168, A:K.224 IPA.4: 5 residues within 4Å: Chain A: N.67, K.68, D.92, I.93, V.94 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.94 Hydrogen bonds: A:D.92 IPA.5: 3 residues within 4Å: Chain A: Y.63, D.90, F.91 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.63, A:F.91 IPA.6: 6 residues within 4Å: Chain A: C.120, S.123, H.125, P.126, V.127, C.150 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.125 IPA.8: 4 residues within 4Å: Chain B: K.60, Y.63, D.90, F.91 No protein-ligand interaction detected (PLIP) IPA.9: 6 residues within 4Å: Chain B: C.120, S.123, H.125, P.126, V.127, C.150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.125 IPA.11: 4 residues within 4Å: Chain C: K.114, K.117, T.118, E.121 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:K.114 IPA.12: 6 residues within 4Å: Chain C: D.220, L.223, K.224, F.227 Chain D: K.168, P.172 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:K.168, C:K.224 IPA.13: 5 residues within 4Å: Chain C: N.67, K.68, D.92, I.93, V.94 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.94 Hydrogen bonds: C:D.92 IPA.14: 3 residues within 4Å: Chain C: Y.63, D.90, F.91 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.63, C:F.91 IPA.15: 6 residues within 4Å: Chain C: C.120, S.123, H.125, P.126, V.127, C.150 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.125 IPA.17: 4 residues within 4Å: Chain D: K.60, Y.63, D.90, F.91 No protein-ligand interaction detected (PLIP) IPA.18: 6 residues within 4Å: Chain D: C.120, S.123, H.125, P.126, V.127, C.150 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zaitsev, V. et al., Insights into the Substrate Specificity of Archaeal Entner-Doudoroff Aldolases: The Structures of Picrophilus torridus 2-Keto-3-deoxygluconate Aldolase and Sulfolobus solfataricus 2-Keto-3-deoxy-6-phosphogluconate Aldolase in Complex with 2-Keto-3-deoxy-6-phosphogluconate. Biochemistry (2018)

Release Date

2018-06-27

Peptides

2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase

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