- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.99 Å
- Oligo State
- homo-tetramer
- Ligands
- 27 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 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)
- 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
AB
BC
CD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.99 Å
- Oligo State
- homo-tetramer
- Ligands
- 27 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 5 x GOL: GLYCEROL(Non-functional Binders)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 1 x GXT: ethanedial(Non-covalent)
- 2 x PYR: PYRUVIC ACID(Covalent)
- 2 x GXP: (4S)-4-hydroxy-2,5-dioxopentanoic acid(Covalent)
- 2 x GXS: (4R)-4-hydroxy-2,5-dioxopentanoic acid(Covalent)
- 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
AB
BC
CD
D