SMTL ID : 3wir.1 (1 other biounit)

Crystal structure of kojibiose phosphorylase complexed with glucose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-dimer

Ligands

4 x BGC: beta-D-glucopyranose(Non-covalent)

BGC.1: 13 residues within 4Å: Chain A: A.329, Y.337, F.342, W.343, D.344, W.391, E.483, K.596, Q.597, S.631, L.633 Ligands: BGC.2, PO4.5 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:W.343, A:K.596, A:Q.597, A:Q.597, A:Q.597 Water bridges: A:A.329, A:A.329, A:D.344 Salt bridges: A:K.596 BGC.2: 9 residues within 4Å: Chain A: Y.337, W.391, E.392, T.401, P.402, T.417, E.483, K.596 Ligands: BGC.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.337, A:W.391, A:E.392, A:E.483, A:E.483, A:K.596 Water bridges: A:E.483 BGC.6: 12 residues within 4Å: Chain B: Y.337, F.342, W.343, D.344, W.391, E.483, K.596, Q.597, S.631, L.633 Ligands: BGC.7, PO4.10 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.337, B:W.343, B:D.344, B:K.596, B:Q.597, B:Q.597, B:Q.597 Water bridges: B:E.483, B:S.632 Salt bridges: B:K.596 BGC.7: 11 residues within 4Å: Chain B: Y.337, F.342, W.391, E.392, T.401, P.402, I.415, T.417, E.483, K.596 Ligands: BGC.6 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.391, B:E.392, B:T.417, B:E.483, B:E.483, B:K.596 Water bridges: B:E.392

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: S.251, R.252, H.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.252 Water bridges: A:R.252, A:D.322 GOL.4: 5 residues within 4Å: Chain A: Y.31, K.131, R.252, E.253, N.319 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.252, A:R.252, A:N.319 Water bridges: A:R.252 GOL.8: 9 residues within 4Å: Chain B: D.291, V.292, N.294, D.296, K.715, F.716, S.717, D.726, R.739 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.290, B:D.296, B:D.726 Water bridges: B:F.716, B:S.717 GOL.9: 4 residues within 4Å: Chain A: F.82 Chain B: C.43, E.44, K.163 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:E.44, A:R.75 Water bridges: A:N.84

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

PO4.5: 6 residues within 4Å: Chain A: Y.337, S.631, S.632, L.633, H.675 Ligands: BGC.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.632 Water bridges: A:K.330, A:N.669, A:N.669, A:H.675 Salt bridges: A:K.330 PO4.10: 6 residues within 4Å: Chain B: Y.337, S.631, S.632, L.633, H.675 Ligands: BGC.6 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:Y.337, B:Y.337, B:S.632 Water bridges: B:K.330, B:Y.337, B:K.596, B:S.632, B:S.632, B:N.669, B:N.669 Salt bridges: B:K.330 PO4.11: 2 residues within 4Å: Chain A: Y.224 Chain B: Y.224 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.224, A:Y.224, B:Y.224 Water bridges: A:Y.224, A:Y.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okada, S. et al., Structural and mutational analysis of substrate recognition in kojibiose phosphorylase. Febs J. (2014)

Release Date

2014-02-05

Peptides

Kojibiose phosphorylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Kojibiose phosphorylase

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