SMTL ID : 6gua.1 (3 other biounits)

Xylulose 5-phosphate phosphoketolase from Lactococcus lactis

Coordinates

PDB Format Compare

Method

SOLUTION SCATTERING 1.95 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 28 residues within 4Å: Chain A: T.58, P.86, H.88, G.146, E.147, L.148, G.172, D.173, G.174, E.175, T.178, D.204, N.206, F.208, K.209, I.210, T.214, K.294, H.323 Chain B: P.442, D.443, E.444, L.484, E.486, Y.508, F.511, V.514 Ligands: MG.2 22 PLIP interactions: 19 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:K.209, A:I.210, A:I.210, B:L.484 Hydrogen bonds: A:T.58, A:T.58, A:G.146, A:L.148, A:D.173, A:G.174, A:E.175, A:N.206, A:F.208, B:E.444 Water bridges: A:T.58, A:H.133 Salt bridges: A:H.88, A:H.88, A:K.294, A:K.294, A:H.323 pi-Stacking: B:F.511 TPP.5: 28 residues within 4Å: Chain A: P.442, D.443, E.444, L.484, E.486, Y.508, F.511, V.514, H.559 Chain B: T.58, P.86, H.88, G.146, E.147, L.148, G.172, D.173, G.174, E.175, T.178, N.206, F.208, K.209, I.210, T.214, K.294, H.323 Ligands: MG.6 21 PLIP interactions: 3 interactions with chain A, 18 interactions with chain B Hydrophobic interactions: A:L.484, A:F.511, B:K.209, B:I.210, B:I.210 Water bridges: A:H.559, B:T.58 Hydrogen bonds: B:T.58, B:T.58, B:G.146, B:L.148, B:D.173, B:G.174, B:E.175, B:N.206, B:F.208 Salt bridges: B:H.88, B:H.88, B:K.294, B:K.294, B:H.323

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: D.173, G.174, N.206, F.208, K.209, T.214, K.294 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.173, A:F.208, H2O.7 MG.6: 8 residues within 4Å: Chain B: D.173, G.174, N.206, F.208, K.209, T.214, K.294 Ligands: TPP.5 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.173, B:F.208, H2O.40

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

PO4.3: 6 residues within 4Å: Chain A: Q.324 Chain B: S.447, R.449, Y.508, H.554, K.608 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.447, B:R.449, B:Y.508, B:Y.508, A:Q.324 Water bridges: B:K.608, B:K.608, B:K.608, B:K.608 Salt bridges: B:H.554, B:K.608 PO4.4: 6 residues within 4Å: Chain A: S.447, R.449, Y.508, H.554, K.608 Chain B: Q.324 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.447, A:S.447, A:R.449, B:Q.324 Water bridges: A:N.555, A:K.608, A:K.608, A:K.608, A:K.608 Salt bridges: A:K.608

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Scheidig, A.J. et al., Crystal structure of a xylulose 5-phosphate phosphoketolase. Insights into the substrate specificity for xylulose 5-phosphate. J.Struct.Biol. (2019)

Release Date

2019-05-22

Peptides

Probable phosphoketolase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable phosphoketolase

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