SMTL ID : 4onv.1

Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.57 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: L.72, F.78, G.106, T.107, G.108, V.131, V.132, I.133, Y.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.72, A:T.107, A:G.108, A:I.133 EDO.7: 5 residues within 4Å: Chain B: F.43, G.47, Q.48, L.49, E.85 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.49 EDO.8: 9 residues within 4Å: Chain B: L.72, F.78, G.106, T.107, G.108, V.131, V.132, I.133, Y.163 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.72, B:G.108, B:I.133 EDO.9: 4 residues within 4Å: Chain B: S.141, E.142, A.143 Ligands: GOL.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.142, B:A.143 EDO.10: 4 residues within 4Å: Chain B: D.196, S.197 Chain D: D.196, S.197 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.197 EDO.16: 9 residues within 4Å: Chain C: L.72, F.78, G.106, T.107, G.108, V.131, V.132, I.133, Y.163 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:L.72, C:R.86, C:T.107, C:G.108, C:V.131, C:I.133 EDO.17: 5 residues within 4Å: Chain C: S.141, E.142, A.143 Chain D: R.313 Ligands: EDO.20 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:S.141, C:E.142, C:A.143, D:R.313 EDO.18: 4 residues within 4Å: Chain C: E.142, A.176, L.177, T.180 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.176 EDO.19: 1 residues within 4Å: Chain C: S.197 No protein-ligand interaction detected (PLIP) EDO.20: 3 residues within 4Å: Chain C: S.141, E.142 Ligands: EDO.17 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.142 EDO.22: 1 residues within 4Å: Chain C: D.50 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.50 EDO.24: 2 residues within 4Å: Chain D: E.84, K.87 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.84, D:K.87, D:K.87 EDO.25: 7 residues within 4Å: Chain C: Q.80, P.305 Chain D: T.110, P.135, Y.136, Y.137, W.138 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:T.110, D:T.110, D:Y.137, D:W.138, C:Q.80 EDO.26: 10 residues within 4Å: Chain D: L.72, F.78, R.86, G.106, T.107, G.108, V.131, V.132, I.133, Y.163 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.72, D:R.86, D:T.107, D:G.108, D:I.133 EDO.28: 3 residues within 4Å: Chain D: S.141, E.142, A.143 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.143

13 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: T.157, P.159, S.186, N.187 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.157, A:S.186 GOL.3: 4 residues within 4Å: Chain A: E.289, V.292, L.293, K.314 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.289, A:E.289, A:L.293, A:K.314 GOL.4: 2 residues within 4Å: Chain A: S.141, E.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.142 GOL.5: 4 residues within 4Å: Chain A: D.280, T.281 Chain B: S.141 Ligands: EDO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.281, A:T.281 GOL.11: 4 residues within 4Å: Chain B: G.82, A.83, E.84, E.85 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.82, B:A.83, B:E.84, B:E.85, B:E.85 GOL.12: 6 residues within 4Å: Chain B: T.33, G.34, L.229, D.234, L.252, R.256 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.33, B:G.34, B:D.234, B:R.256 GOL.13: 5 residues within 4Å: Chain B: E.84, K.87, A.88, R.91, H.121 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.84, B:R.91, B:H.121 GOL.14: 2 residues within 4Å: Chain B: Q.171, D.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.172, B:D.172 GOL.21: 5 residues within 4Å: Chain C: A.182, D.183, S.184, R.185, S.186 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.183, C:S.186 GOL.27: 2 residues within 4Å: Chain D: D.60, R.296 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.60, D:R.296, D:R.296 GOL.29: 4 residues within 4Å: Chain D: A.182, D.183, R.185, S.186 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.182, D:S.186 GOL.30: 5 residues within 4Å: Chain D: T.33, G.34, D.234, W.255, R.256 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:G.34, D:W.255, D:R.256 GOL.31: 4 residues within 4Å: Chain D: K.87, A.88, R.91, H.121 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.87

4 x KDG: 2-KETO-3-DEOXYGLUCONATE(Covalent)

KDG.6: 14 residues within 4Å: Chain A: P.38, F.70, G.73, S.74, G.75, Y.163, F.165, K.192, T.194, G.220, Y.221, I.237, S.238, A.239 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:P.38, A:P.38, A:K.192, A:I.237 Hydrogen bonds: A:S.74, A:G.75, A:Y.163, A:K.192, A:T.194, A:A.239 Salt bridges: A:K.192 KDG.15: 13 residues within 4Å: Chain B: P.38, F.70, G.73, S.74, G.75, Y.163, K.192, T.194, G.220, I.237, S.238, A.239, F.283 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:P.38, B:P.38, B:K.192 Hydrogen bonds: B:S.74, B:G.75, B:Y.163, B:T.194, B:G.220, B:A.239 Water bridges: B:D.222 Salt bridges: B:K.192 KDG.23: 13 residues within 4Å: Chain C: P.38, F.70, G.73, S.74, G.75, Y.163, F.165, K.192, T.194, G.220, I.237, S.238, A.239 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:P.38, C:P.38, C:K.192, C:I.237 Hydrogen bonds: C:S.74, C:G.75, C:Y.163, C:T.194, C:T.194, C:A.239 Salt bridges: C:K.192 KDG.32: 15 residues within 4Å: Chain D: P.38, F.70, G.73, S.74, G.75, Y.163, F.165, K.192, T.194, G.220, Y.221, I.237, S.238, A.239, F.283 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:P.38, D:P.38, D:K.192 Hydrogen bonds: D:S.74, D:G.75, D:Y.163, D:K.192, D:T.194, D:A.239 Water bridges: D:D.222, D:Y.277 Salt bridges: D:K.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manoj Kumar, P. et al., Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate. To be Published

Release Date

2015-01-14

Peptides

Probable 2-keto-3-deoxy-galactonate aldolase YagE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Probable 2-keto-3-deoxy-galactonate aldolase YagE

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