SMTL ID : 4uxd.1

2-keto 3-deoxygluconate aldolase from Picrophilus torridus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

19 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 11 residues within 4Å: Chain A: P.31, F.63, G.66, S.67, T.68, Y.154, S.184, G.207, V.224 Ligands: GOL.2, IPA.3 Ligand excluded by PLIP GOL.2: 13 residues within 4Å: Chain A: P.31, T.68, G.207, Q.208, D.209, V.224, C.225, G.226, T.227, M.260, Y.272 Ligands: GOL.1, IPA.3 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: K.130, L.131, N.132, Q.133, K.162 Ligand excluded by PLIP GOL.6: 9 residues within 4Å: Chain A: Y.127, Y.128, K.130, F.159, T.160, N.161 Chain B: Q.158, F.159 Ligands: GOL.13 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: R.189, M.192, E.193 Chain D: I.257 Ligands: EDO.24 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: N.155, P.157, K.162, I.163, D.164, P.165, G.190, M.194 Ligand excluded by PLIP GOL.9: 11 residues within 4Å: Chain B: P.31, F.63, G.66, S.67, T.68, Y.154, K.182, S.184, G.207, V.224 Ligands: GOL.10 Ligand excluded by PLIP GOL.10: 12 residues within 4Å: Chain B: P.31, T.68, G.207, D.209, V.224, C.225, G.226, M.260, F.268, Y.272 Ligands: GOL.9, IPA.11 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: N.132, Q.133, K.162, D.164 Ligand excluded by PLIP GOL.13: 9 residues within 4Å: Chain A: Y.128, Q.158, F.159 Chain B: Y.127, Y.128, F.159, T.160, N.161 Ligands: GOL.6 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain B: D.164, P.165, G.190, E.193, M.194 Ligand excluded by PLIP GOL.16: 11 residues within 4Å: Chain C: P.31, F.63, G.66, S.67, T.68, Y.154, S.184, G.207, V.224 Ligands: EDO.17, PGE.18 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain B: R.189, M.192, E.193 Chain C: D.210, I.257, K.261 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain C: L.131, N.132, Q.133, K.162 Ligand excluded by PLIP GOL.21: 11 residues within 4Å: Chain D: P.31, F.63, G.66, S.67, T.68, Y.154, S.184, G.207, V.224 Ligands: EDO.22, GOL.23 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain D: I.156, F.159, S.184, Q.208, F.268 Ligands: GOL.21, EDO.22 Ligand excluded by PLIP GOL.26: 6 residues within 4Å: Chain C: N.104 Chain D: H.39, G.40, N.41, R.287, P.288 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain D: K.130, L.131, N.132, Q.133, K.162 Ligand excluded by PLIP GOL.28: 9 residues within 4Å: Chain C: Q.158, F.159 Chain D: Y.127, Y.128, K.130, F.159, T.160, N.161 Ligands: IPA.29 Ligand excluded by PLIP

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

IPA.3: 6 residues within 4Å: Chain A: Q.158, F.159, Q.208, F.268 Ligands: GOL.1, GOL.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.158, A:F.159, A:F.268 Hydrogen bonds: A:Q.208 IPA.11: 4 residues within 4Å: Chain B: Q.158, Q.208, F.268 Ligands: GOL.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.268 Hydrogen bonds: B:Q.208 IPA.29: 6 residues within 4Å: Chain D: K.130, P.157, T.160, N.161, K.162 Ligands: GOL.28 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:K.162

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: D.37, N.41 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.37 EDO.17: 11 residues within 4Å: Chain C: P.31, G.207, D.209, V.224, C.225, G.226, T.227, M.260, Y.272 Ligands: GOL.16, PGE.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:V.224, C:G.226, C:T.227, C:Y.272 EDO.22: 10 residues within 4Å: Chain D: G.207, D.209, V.224, C.225, G.226, T.227, M.260, Y.272 Ligands: GOL.21, GOL.23 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.224, D:G.226, D:T.227 EDO.24: 6 residues within 4Å: Chain A: R.189 Chain D: D.210, I.257, M.260, K.261 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.189 EDO.25: 3 residues within 4Å: Chain D: I.42, D.43, Y.44 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.43, D:D.43, D:Y.44

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.15: 5 residues within 4Å: Chain B: D.187, R.189 Chain C: S.185, A.186, D.187 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.189

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.18: 8 residues within 4Å: Chain C: Y.154, I.156, Q.158, F.159, Q.208, F.268 Ligands: GOL.16, EDO.17 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.154, C:S.184, C:Q.208

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

2015-09-30

Peptides

2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

2-DEHYDRO-3-DEOXY-D-GLUCONATE/2-DEHYDRO-3-DEOXY-PHOSPHOGLUCONATE ALDOLASE