SMTL ID : 4zlg.1

Cellobionic acid phosphorylase - gluconic acid complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x GCO: D-gluconic acid(Non-covalent)

GCO.1: 10 residues within 4Å: Chain A: Q.347, I.398, D.472, R.609, K.613, E.619 Chain B: W.167, Q.190 Ligands: GOL.2, LGC.4 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.472, A:D.472, A:K.613, A:K.613, B:Q.190 Salt bridges: A:R.609, A:K.613 GCO.8: 10 residues within 4Å: Chain A: W.167, Q.190 Chain B: Q.347, I.398, D.472, R.609, K.613, E.619 Ligands: GOL.9, LGC.11 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.472, B:K.613, B:K.613, A:Q.190 Salt bridges: B:R.609, B:K.613

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 9 residues within 4Å: Chain A: T.343, D.345, P.346, Q.347, K.396, Y.397, I.398, N.399 Ligands: GCO.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:T.343, A:T.343, A:Q.347, A:Q.347, A:N.399 Water bridges: A:T.343, A:I.398 GOL.3: 8 residues within 4Å: Chain A: G.1, L.2, L.13, S.15, A.18, M.19, E.657, L.660 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.1 GOL.9: 9 residues within 4Å: Chain B: T.343, D.345, P.346, Q.347, K.396, Y.397, I.398, N.399 Ligands: GCO.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.343, B:Q.347, B:Q.347, B:N.399 Water bridges: B:T.343, B:T.343, B:I.398 GOL.10: 8 residues within 4Å: Chain B: G.1, L.2, L.13, S.15, A.18, M.19, E.657, L.660 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.1

2 x LGC: D-glucono-1,5-lactone(Non-covalent)

LGC.4: 12 residues within 4Å: Chain A: R.341, Q.347, R.349, N.350, W.470, C.471, D.472, P.473, E.619, Y.624 Ligands: GCO.1, SO4.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.341, A:R.349, A:R.349, A:N.350, A:N.350, A:D.472, A:E.619 Water bridges: A:Y.624, A:Y.624, A:N.672, A:N.672 LGC.11: 12 residues within 4Å: Chain B: R.341, Q.347, R.349, N.350, W.470, C.471, D.472, P.473, E.619, Y.624 Ligands: GCO.8, SO4.12 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:R.341, B:R.349, B:R.349, B:N.350, B:N.350, B:D.472, B:Y.624 Water bridges: B:Y.624, B:H.626, B:N.672, B:N.672

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 7 residues within 4Å: Chain A: R.341, Y.624, H.626, N.672, T.694, G.695 Ligands: LGC.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.624, A:T.694, A:G.695 Water bridges: A:R.341, A:H.626, A:N.672, A:N.672 Salt bridges: A:R.341, A:H.626 SO4.6: 4 residues within 4Å: Chain A: Q.12, N.104, S.106, H.117 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.104, A:S.106 Water bridges: A:Q.12, A:Q.12, A:Q.12, A:Q.12, A:H.117 Salt bridges: A:H.117 SO4.12: 7 residues within 4Å: Chain B: R.341, Y.624, H.626, N.672, T.694, G.695 Ligands: LGC.11 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Y.624, B:Y.624, B:G.695 Water bridges: B:R.341, B:N.350, B:N.672, B:N.672, B:T.696 Salt bridges: B:R.341, B:H.626 SO4.13: 4 residues within 4Å: Chain B: Q.12, N.104, S.106, H.117 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.104, B:S.106 Water bridges: B:Q.12, B:Q.12, B:Q.12, B:Q.12 Salt bridges: B:H.117

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 5 residues within 4Å: Chain A: W.470, C.471, R.538, N.560, M.595 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain B: W.470, C.471, R.538, N.560, M.595 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nam, Y.W. et al., Crystal Structure and Substrate Recognition of Cellobionic Acid Phosphorylase, Which Plays a Key Role in Oxidative Cellulose Degradation by Microbes. J.Biol.Chem. (2015)

Release Date

2015-06-10

Peptides

Putative b-glycan phosphorylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative b-glycan phosphorylase

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