SMTL ID : 5xsf.1

Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4 with 3-phosphoglycerate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-trimer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 9 residues within 4Å: Chain A: E.42, R.46, G.68, T.69, V.88, S.89, P.90, K.129 Chain B: V.148 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.69, A:S.89 Water bridges: A:R.46, A:K.129 Salt bridges: A:R.46, A:K.129 PO4.2: 2 residues within 4Å: Chain A: R.10, R.153 3 PLIP interactions: 3 interactions with chain A Water bridges: A:P.172 Salt bridges: A:R.10, A:R.153 PO4.5: 9 residues within 4Å: Chain B: E.42, R.46, G.68, T.69, V.88, S.89, P.90, K.129 Chain C: V.148 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.69, B:S.89 Water bridges: B:R.46, B:K.129 Salt bridges: B:R.46, B:K.129 PO4.6: 2 residues within 4Å: Chain B: R.10, R.153 3 PLIP interactions: 3 interactions with chain B Water bridges: B:P.172 Salt bridges: B:R.10, B:R.153 PO4.9: 9 residues within 4Å: Chain A: V.148 Chain C: E.42, R.46, G.68, T.69, V.88, S.89, P.90, K.129 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.69, C:S.89 Water bridges: C:R.46, C:K.129 Salt bridges: C:R.46, C:K.129 PO4.10: 2 residues within 4Å: Chain C: R.10, R.153 3 PLIP interactions: 3 interactions with chain C Water bridges: C:P.172 Salt bridges: C:R.10, C:R.153

3 x 3PG: 3-PHOSPHOGLYCERIC ACID(Non-covalent)

3PG.3: 6 residues within 4Å: Chain A: V.17, R.46, T.157, G.158, G.159, S.180 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.159, A:S.180, A:S.180 Water bridges: A:R.46, A:R.46, A:I.160, A:S.180, A:W.181 Salt bridges: A:R.46 3PG.7: 6 residues within 4Å: Chain B: V.17, R.46, T.157, G.158, G.159, S.180 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:G.159, B:S.180, B:S.180 Water bridges: B:R.46, B:R.46, B:I.160, B:S.180, B:W.181 Salt bridges: B:R.46 3PG.11: 6 residues within 4Å: Chain C: V.17, R.46, T.157, G.158, G.159, S.180 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:G.159, C:S.180, C:S.180 Water bridges: C:R.46, C:R.46, C:I.160, C:S.180, C:W.181 Salt bridges: C:R.46

3 x 3PY: 3-HYDROXYPYRUVIC ACID(Non-covalent)

3PY.4: 9 residues within 4Å: Chain A: V.19, I.20, E.21, D.22, D.25, I.29, V.183, P.184, G.186 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.19, A:E.21, A:D.22, A:D.22, A:D.25, A:G.186 3PY.8: 9 residues within 4Å: Chain B: V.19, I.20, E.21, D.22, D.25, I.29, V.183, P.184, G.186 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:V.19, B:E.21, B:D.22, B:D.22, B:G.186 3PY.12: 9 residues within 4Å: Chain C: V.19, I.20, E.21, D.22, D.25, I.29, V.183, P.184, G.186 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:V.19, C:E.21, C:D.22, C:D.22, C:D.25, C:G.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seo, P.W. et al., Crystal structure of the 2-keto-3-deoxy-6-phosphogluconate aldolase of Zymomonas mobilis ZM4. To Be Published

Release Date

2018-06-20

Peptides

KHG/KDPG aldolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

KHG/KDPG aldolase