SMTL ID : 4oe7.1

Crystal structure of YagE, a KDG aldolase protein, in complex with aldol condensed product of pyruvate and glyoxal

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 10 residues within 4Å: Chain A: L.72, F.78, R.86, G.106, T.107, G.108, V.131, V.132, I.133, Y.163 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: D.67, V.249, L.252, K.253, R.256 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: L.72, R.86, K.87, A.90, I.105, L.118, H.121, A.122 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: T.110, P.135, Y.136, Y.137, W.138 Chain B: Q.80, P.305 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: D.196, Y.221, D.223, H.224 Chain C: A.199, R.202 Ligand excluded by PLIP EDO.8: 3 residues within 4Å: Chain A: T.174, P.175, A.176 Ligand excluded by PLIP EDO.11: 9 residues within 4Å: Chain B: L.72, F.78, R.86, G.106, T.107, G.108, V.131, V.132, I.133 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain B: K.262, G.265, Y.266 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: F.165, A.167, I.195, D.196, Y.221 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain B: G.82, A.83, E.84, E.85 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: R.113 Chain B: G.47, H.301, L.303, P.304 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain A: Q.80, P.305 Chain B: T.110, P.135, Y.136, Y.137, W.138 Ligand excluded by PLIP EDO.22: 10 residues within 4Å: Chain C: L.72, F.78, R.86, G.106, T.107, G.108, V.131, V.132, I.133, Y.163 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain C: L.72, R.86, K.87, A.90, I.105, L.118, H.121, A.122 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain C: T.174, P.175, A.176 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: A.199, R.202 Chain C: D.196, Y.221, D.223, H.224 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain C: I.42, D.50, G.53, P.297, V.298, S.299 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain C: A.167, I.195, D.196, Y.221 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain A: Q.275, Q.278 Chain C: A.199, R.202, S.203 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain C: G.170, Q.171, D.172 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain C: P.304, P.305 Chain D: N.144, R.147, Y.148, Q.151 Ligand excluded by PLIP EDO.34: 10 residues within 4Å: Chain C: K.139, L.168, T.169, G.170 Chain D: K.139, P.166, A.167, L.168, T.169, G.170 Ligand excluded by PLIP EDO.35: 7 residues within 4Å: Chain B: A.199, R.202 Chain D: D.196, Y.221, D.223, H.224, P.274 Ligand excluded by PLIP EDO.36: 9 residues within 4Å: Chain D: L.72, F.78, R.86, G.106, T.107, G.108, V.131, V.132, I.133 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain D: T.174, P.175, A.176 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain D: D.60, L.61, N.242, P.245, R.296 Ligand excluded by PLIP EDO.41: 5 residues within 4Å: Chain D: F.165, A.167, I.195, D.196, Y.221 Ligand excluded by PLIP

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: E.84, K.87, A.88, R.91, H.121 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.87, A:R.91 GOL.12: 5 residues within 4Å: Chain B: G.47, Q.48, L.49, E.85, I.89 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.47, B:L.49, B:E.85, A:R.113 GOL.13: 5 residues within 4Å: Chain B: S.197, A.199, H.200, S.203 Chain D: Q.278 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.197, B:S.197 GOL.23: 5 residues within 4Å: Chain C: D.67, V.249, L.252, K.253, R.256 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.67, C:V.249, C:K.253, C:R.256 GOL.39: 3 residues within 4Å: Chain D: G.170, Q.171, D.172 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.172

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: P.38, G.75 Ligands: GXT.9, PYR.10 2 PLIP interactions: 2 Ligand-Ligand interactions Metal complexes: GXT.9, PYR.10 MG.15: 5 residues within 4Å: Chain B: P.38, G.75, A.239 Ligands: GXP.20, GXS.21 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain C: P.38, G.75 Ligands: PYR.33 1 PLIP interactions: 1 Ligand-Ligand interactions Metal complexes: PYR.33 MG.40: 5 residues within 4Å: Chain D: P.38, G.75, A.239 Ligands: GXP.42, GXS.43 No protein-ligand interaction detected (PLIP)

1 x GXT: ethanedial(Non-covalent)

GXT.9: 7 residues within 4Å: Chain A: S.74, G.75, F.165, T.194, Y.221 Ligands: MG.4, PYR.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.75

2 x PYR: PYRUVIC ACID(Covalent)

PYR.10: 11 residues within 4Å: Chain A: P.38, F.70, G.73, S.74, G.75, Y.163, K.192, G.220, I.237 Ligands: MG.4, GXT.9 8 PLIP interactions: 8 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 Water bridges: A:S.74 Salt bridges: A:K.192 PYR.33: 10 residues within 4Å: Chain C: P.38, F.70, G.73, S.74, G.75, Y.163, K.192, G.220, I.237 Ligands: MG.24 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:P.38, C:K.192 Hydrogen bonds: C:S.74, C:G.75, C:Y.163 Water bridges: C:S.74, C:S.74 Salt bridges: C:K.192

2 x GXP: (4S)-4-hydroxy-2,5-dioxopentanoic acid(Covalent)

GXP.20: 13 residues within 4Å: Chain B: P.38, F.70, G.73, S.74, G.75, Y.163, F.165, K.192, T.194, G.220, I.237 Ligands: MG.15, GXS.21 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:P.38, B:K.192 Hydrogen bonds: B:S.74, B:S.74, B:G.75, B:Y.163, B:T.194 Salt bridges: B:K.192 GXP.42: 14 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, I.237, F.283 Ligands: MG.40, GXS.43 8 PLIP interactions: 8 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:T.194 Salt bridges: D:K.192

2 x GXS: (4R)-4-hydroxy-2,5-dioxopentanoic acid(Covalent)

GXS.21: 15 residues within 4Å: Chain B: P.38, F.70, G.73, S.74, G.75, Y.163, F.165, K.192, T.194, G.220, I.237, A.239, F.283 Ligands: MG.15, GXP.20 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:P.38, B:K.192 Hydrogen bonds: B:S.74, B:G.75, B:Y.163, B:Y.163 Salt bridges: B:K.192 GXS.43: 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, F.283 Ligands: MG.40, GXP.42 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:P.38, D:K.192 Hydrogen bonds: D:S.74, D:G.75, D:Y.163, D:T.194 Water bridges: D:P.38 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 aldol condensed product of pyruvate and glyoxal. To be Published

Release Date

2014-12-24

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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