SMTL ID : 1q6r.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.76 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.33, D.62, K.64 Ligands: LX1.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.33, A:D.62, H2O.5, H2O.6 MG.3: 4 residues within 4Å: Chain B: E.33, D.62, K.64 Ligands: LX1.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.33, B:D.62, H2O.9, H2O.12 MG.5: 4 residues within 4Å: Chain C: E.33, D.62, K.64 Ligands: LX1.6 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.33, C:D.62, H2O.16, H2O.18 MG.7: 4 residues within 4Å: Chain D: E.33, D.62, K.64 Ligands: LX1.8 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.33, D:D.62, H2O.21, H2O.24

4 x LX1: L-XYLULOSE 5-PHOSPHATE(Non-covalent)

LX1.2: 15 residues within 4Å: Chain A: A.9, D.11, E.33, D.62, K.64, H.136, T.169, G.170, G.171, I.189, A.190, G.191, R.192 Chain B: D.67 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A 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:L.172, A:L.172, A:L.172, A:R.192, A:R.192, A:S.193, A:R.195, A:R.195 Salt bridges: A:R.192 LX1.4: 15 residues within 4Å: Chain A: D.67 Chain B: A.9, D.11, E.33, D.62, K.64, H.136, T.169, G.170, G.171, I.189, A.190, G.191, R.192 Ligands: MG.3 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:D.11, 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.169, B:T.169, B:R.192, B:S.193, B:R.195, B:R.195 Salt bridges: B:R.192 LX1.6: 15 residues within 4Å: Chain C: A.9, D.11, E.33, D.62, K.64, H.136, T.169, G.170, G.171, I.189, A.190, G.191, R.192 Chain D: D.67 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:K.64, C:T.169, C:G.171, C:G.191, C:R.192 Water bridges: C:T.169, C:T.169, C:L.172, C:R.192, C:R.192, C:S.193, C:R.195, C:R.195 Salt bridges: C:R.192 LX1.8: 15 residues within 4Å: Chain C: D.67 Chain D: A.9, D.11, E.33, D.62, K.64, H.136, T.169, G.170, G.171, I.189, A.190, G.191, R.192 Ligands: MG.7 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:K.64, D:T.169, D:T.169, D:G.171, D:G.191, D:R.192 Water bridges: D:L.172, D:L.172, D:R.192, D:S.193, D:R.195, D:R.195 Salt bridges: D: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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

3-keto-L-gulonate 6-phosphate decarboxylase

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