SMTL ID : 4ptn.1

Crystal Structure of YagE, a KDG aldolase protein in complex with Magnesium cation coordinated L-glyceraldehyde

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 11 residues within 4Å: Chain A: F.70, L.72, G.73, 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.2: 7 residues within 4Å: Chain A: D.196, Y.221, D.223, H.224, P.274 Chain C: A.199, R.202 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:H.224, C:R.202, C:R.202 EDO.5: 11 residues within 4Å: Chain B: F.70, L.72, G.73, F.78, G.106, T.107, G.108, V.131, V.132, I.133, Y.163 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.72, B:T.107, B:G.108, B:I.133 EDO.6: 7 residues within 4Å: Chain B: D.196, Y.221, D.223, H.224, P.274 Chain D: A.199, R.202 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.202, D:R.202 EDO.7: 6 residues within 4Å: Chain B: V.247, Y.266, T.269, L.324, K.325, L.326 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.269, B:K.325 EDO.8: 6 residues within 4Å: Chain B: F.165, A.167, I.195, D.196, Y.221 Ligands: GOL.9 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.196 EDO.13: 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 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.72, C:T.107, C:G.108, C:I.133 EDO.14: 7 residues within 4Å: Chain A: A.199, R.202 Chain C: D.196, Y.221, D.223, H.224, P.274 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:H.224, A:R.202, A:R.202 EDO.15: 4 residues within 4Å: Chain C: G.82, A.83, E.84, E.85 6 PLIP interactions: 1 interactions with chain D, 5 interactions with chain C Water bridges: D:E.114 Hydrogen bonds: C:G.82, C:G.82, C:A.83, C:E.84, C:E.85 EDO.18: 7 residues within 4Å: Chain B: A.199, R.202 Chain D: D.196, Y.221, D.223, H.224, P.274 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.202, B:R.202 EDO.19: 9 residues within 4Å: Chain D: L.72, F.78, R.86, G.106, T.107, G.108, V.131, V.132, I.133 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

4 x GXV: L-glyceraldehyde(Non-covalent)

GXV.3: 9 residues within 4Å: Chain A: P.38, F.165, K.192, T.194, G.220, Y.221, S.238, A.239 Ligands: MG.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.192, A:Y.221, A:A.239 Water bridges: A:Y.163 GXV.10: 9 residues within 4Å: Chain B: P.38, F.165, K.192, T.194, G.220, Y.221, S.238, A.239 Ligands: MG.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.192, B:Y.221, B:Y.221, B:A.239 Water bridges: B:Y.163, B:D.222, B:D.222 GXV.16: 10 residues within 4Å: Chain C: P.38, F.165, K.192, T.194, G.220, Y.221, S.238, A.239, F.283 Ligands: MG.17 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:K.192, C:A.239 Water bridges: C:G.75, C:D.222, C:D.222 GXV.20: 10 residues within 4Å: Chain D: K.192, T.194, G.220, Y.221, D.222, I.237, S.238, A.239, F.283 Ligands: MG.21 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.192, D:D.222, D:A.239

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: P.38, G.75 Ligands: GXV.3 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: P.38, G.75 Ligands: GXV.10 No protein-ligand interaction detected (PLIP) MG.17: 3 residues within 4Å: Chain C: P.38, G.75 Ligands: GXV.16 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain D: P.38, G.75 Ligands: GXV.20 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 5 residues within 4Å: Chain B: D.196, S.197 Chain D: D.196, S.197 Ligands: EDO.8 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:S.197 Water bridges: D:D.196, B:S.197

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.12: 6 residues within 4Å: Chain A: A.143 Chain B: D.280, S.307, P.308, L.309, D.310 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:D.310 Hydrogen bonds: B:D.310 Water bridges: B:D.280, B:D.310, B:D.310 Salt bridges: B:R.313, A:R.147 PYR.22: 6 residues within 4Å: Chain C: A.143 Chain D: D.280, S.307, P.308, L.309, D.310 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:D.310 Hydrogen bonds: D:D.310 Water bridges: D:D.310, D:D.310 Salt bridges: D:R.313, C:R.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manicka, S. et al., Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12. Proteins (2008)

Release Date

2014-12-03

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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