SMTL ID : 1so4.2 (1 other biounit)

Crystal structure of K64A mutant of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-threonohydroxamate 4-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.33, D.62 Ligands: TX4.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.33, A:D.62, H2O.11, H2O.12 MG.3: 3 residues within 4Å: Chain B: E.33, D.62 Ligands: TX4.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.33, B:D.62, H2O.22, H2O.22 MG.5: 3 residues within 4Å: Chain C: E.33, D.62 Ligands: TX4.6 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.33, C:D.62, H2O.33, H2O.33 MG.7: 3 residues within 4Å: Chain D: E.33, D.62 Ligands: TX4.8 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.33, D:D.62, H2O.43, H2O.44

4 x TX4: L-THREONOHYDROXAMATE 4-PHOSPHATE(Non-covalent)

TX4.2: 14 residues within 4Å: Chain A: A.9, D.11, E.33, D.62, H.136, T.169, G.170, G.171, I.189, A.190, G.191, R.192 Chain B: D.67 Ligands: MG.1 19 PLIP interactions: 17 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.11, A:T.169, A:T.169, A:G.171, A:G.191, A:R.192, B:D.67 Water bridges: A:T.36, A:T.36, A:E.112, A:T.114, A:R.139, A:R.139, A:R.139, A:R.139, A:R.192, A:S.193, B:D.67 Salt bridges: A:R.192 TX4.4: 14 residues within 4Å: Chain A: D.67 Chain B: A.9, D.11, E.33, D.62, H.136, T.169, G.170, G.171, I.189, A.190, G.191, R.192 Ligands: MG.3 18 PLIP interactions: 1 interactions with chain A, 17 interactions with chain B Hydrogen bonds: A:D.67, B:D.11, B:T.169, B:G.171, B:G.191, B:R.192 Water bridges: B:T.36, B:T.36, B:R.139, B:R.139, B:R.139, B:R.139, B:T.169, B:T.169, B:R.192, B:S.193 Salt bridges: B:R.139, B:R.192 TX4.6: 14 residues within 4Å: Chain C: A.9, D.11, E.33, D.62, H.136, T.169, G.170, G.171, I.189, A.190, G.191, R.192 Chain D: D.67 Ligands: MG.5 15 PLIP interactions: 1 interactions with chain D, 14 interactions with chain C Water bridges: D:D.67, C:E.112, C:E.112, C:R.139, C:R.139, C:R.139, C:R.139, C:R.192, C:S.193 Hydrogen bonds: C:H.136, C:T.169, C:G.171, C:G.191, C:R.192 Salt bridges: C:R.192 TX4.8: 14 residues within 4Å: Chain C: D.67 Chain D: A.9, D.11, E.33, D.62, H.136, T.169, G.170, G.171, I.189, A.190, G.191, R.192 Ligands: MG.7 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:T.169, D:T.169, D:G.171, D:G.191, D:R.192, C:D.67, C:D.67 Water bridges: D:D.62, D:D.62, D:D.62, D:D.62, D:R.139, D:R.139, D:R.139, D:R.139, D:L.172, D:L.172, D:R.192, D:S.193 Salt bridges: D:R.139, D:R.192

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: Crystallographic Evidence for a Proton Relay System in the Active Site of 3-Keto-l-gulonate 6-Phosphate Decarboxylase(,). Biochemistry (2004)

Release Date

2004-06-08

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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