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

Crystal structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound D-ribulose 5-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-tetramer

Ligands

4 x 5RP: D-ribulose 5-phosphate(Non-covalent)

5RP.1: 17 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, L.172, I.189, A.190, G.191, R.192 Chain B: D.67 Ligands: MG.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:D.11, A:D.11, A:K.64, A:H.136, A:G.171, A:L.172, A:G.191, A:R.192 Water bridges: A:T.36, A:T.36, A:R.139, A:R.139, A:G.170, A:R.192, A:R.192, A:S.193 Salt bridges: A:R.192 5RP.2: 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.4 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:D.11, B:D.11, B:K.64, B:K.64, B:H.136, B:G.171, B:L.172, B:G.191, B:R.192 Water bridges: B:T.36, B:T.36, B:R.139, B:T.169, B:T.169, B:S.193, B:R.195 Salt bridges: B:R.192 5RP.5: 17 residues within 4Å: Chain C: A.9, D.11, E.33, D.62, K.64, H.136, R.139, T.169, G.170, G.171, L.172, I.189, A.190, G.191, R.192 Chain D: D.67 Ligands: MG.7 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:D.11, C:K.64, C:H.136, C:G.171, C:L.172, C:G.191, C:R.192 Water bridges: C:T.36, C:R.139, C:R.139, C:T.169, C:T.169, C:R.192, C:R.192, C:S.193 Salt bridges: C:R.192 5RP.6: 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.8 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:D.11, D:K.64, D:K.64, D:H.136, D:G.171, D:L.172, D:G.191, D:R.192 Water bridges: D:T.36, D:D.62, D:D.62, D:D.62, D:D.62, D:R.139, D:G.170, D:S.193, D:R.195 Salt bridges: D:R.192

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.33, D.62, K.64 Ligands: 5RP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.33, A:D.62, H2O.200, H2O.203 MG.4: 4 residues within 4Å: Chain B: E.33, D.62, K.64 Ligands: 5RP.2 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.33, B:D.62, H2O.407, H2O.412 MG.7: 4 residues within 4Å: Chain C: E.33, D.62, K.64 Ligands: 5RP.5 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.33, C:D.62, H2O.625, H2O.628 MG.8: 4 residues within 4Å: Chain D: E.33, D.62, K.64 Ligands: 5RP.6 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.33, D:D.62, H2O.832, H2O.837

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wise, E.L. et al., Evolution of enzymatic activities in the orotidine 5'-monophosphate decarboxylase suprafamily: structural basis for catalytic promiscuity in wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate decarboxylase. Biochemistry (2005)

Release Date

2005-04-26

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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