SMTL ID : 1q6q.1 (1 other biounit)

Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound xylitol 5-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.33, D.62 Ligands: LXP.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.33, A:D.62, H2O.3, H2O.9 MG.3: 3 residues within 4Å: Chain B: E.33, D.62 Ligands: LXP.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.33, B:D.62, H2O.12, H2O.16

2 x LXP: L-XYLITOL 5-PHOSPHATE(Non-covalent)

LXP.2: 16 residues within 4Å: Chain A: A.9, D.11, E.33, D.62, K.64, H.136, R.139, T.169, G.170, G.171, I.189, A.190, G.191, R.192 Chain B: D.67 Ligands: MG.1 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.11, A:K.64, A:T.169, A:T.169, A:G.171, A:G.191, A:R.192 Water bridges: A:T.36, A:T.36, A:T.36, A:T.36, A:T.36, A:R.139, A:R.139, A:L.172, A:L.172, A:R.192, A:S.193, A:S.193, B:D.67 Salt bridges: A:R.192 LXP.4: 16 residues within 4Å: Chain A: D.67 Chain B: A.9, D.11, E.33, D.62, K.64, H.136, R.139, T.169, G.170, G.171, I.189, A.190, G.191, R.192 Ligands: MG.3 20 PLIP interactions: 19 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.64, B:T.169, B:G.171, B:G.191, B:R.192 Water bridges: B:T.36, B:T.36, B:T.36, B:D.62, B:R.139, B:R.139, B:R.139, B:T.169, B:T.169, B:L.172, B:R.192, B:S.193, A:D.67 Salt bridges: B:R.139, B:R.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wise, E.L. et al., Structural Evidence for a 1,2-Enediolate Intermediate in the Reaction Catalyzed by 3-Keto-l-Gulonate 6-Phosphate Decarboxylase, a Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily. Biochemistry (2003)

Release Date

2003-10-28

Peptides

3-keto-L-gulonate 6-phosphate decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

3-keto-L-gulonate 6-phosphate decarboxylase

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