SMTL ID : 5ayc.1

Crystal structure of Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1) in complexes with sulfate and 4-O-beta-D-mannosyl-D-glucose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-trimer

Ligands

3 x BGC- BMA: beta-D-mannopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

BGC-BMA.1: 15 residues within 4Å: Chain A: N.71, R.86, R.92, Y.128, D.129, E.147, R.188, N.189, F.211, I.212, Y.281, V.316, F.321, D.341 Ligands: SO4.2 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.86, A:R.86, A:R.92, A:R.92, A:N.71, A:R.86, A:D.129 Water bridges: A:N.126, A:E.147, A:Y.281, B:R.273, B:R.273, B:R.273, A:D.341 Salt bridges: A:R.92 BGC-BMA.3: 15 residues within 4Å: Chain B: N.71, R.86, R.92, Y.128, D.129, E.147, R.188, N.189, F.211, I.212, Y.281, V.316, F.321, D.341 Ligands: SO4.4 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.86, B:R.86, B:R.92, B:R.92, B:N.71, B:R.86, B:D.129 Water bridges: B:N.126, B:E.147, B:Y.281, C:R.273, C:R.273, C:R.273, B:D.341 Salt bridges: B:R.92 BGC-BMA.5: 15 residues within 4Å: Chain C: N.71, R.86, R.92, Y.128, D.129, E.147, R.188, N.189, F.211, I.212, Y.281, V.316, F.321, D.341 Ligands: SO4.6 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:R.86, C:R.86, C:R.92, C:R.92, C:N.71, C:R.86, C:D.129 Water bridges: C:N.126, C:Y.281, A:H.245, A:R.273, A:R.273, A:R.273, C:D.341 Salt bridges: C:R.92

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

SO4.2: 8 residues within 4Å: Chain A: R.188, N.189, R.206, K.251, H.270, Y.281 Ligands: BGC-BMA.1, BGC-BMA.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.189, A:N.189, A:Y.281 Water bridges: A:Y.281 Salt bridges: A:R.188, A:R.206, A:K.251, A:H.270 SO4.4: 8 residues within 4Å: Chain B: R.188, N.189, R.206, K.251, H.270, Y.281 Ligands: BGC-BMA.3, BGC-BMA.3 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.189, B:N.189, B:Y.281 Water bridges: B:Y.281 Salt bridges: B:R.188, B:R.206, B:K.251, B:H.270 SO4.6: 8 residues within 4Å: Chain C: R.188, N.189, R.206, K.251, H.270, Y.281 Ligands: BGC-BMA.5, BGC-BMA.5 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.189, C:N.189, C:Y.281 Water bridges: C:Y.281 Salt bridges: C:R.188, C:R.206, C:K.251, C:H.270

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ye, Y. et al., Structural insights into the difference in substrate recognition of two mannoside phosphorylases from two GH130 subfamilies. Febs Lett. (2016)

Release Date

2016-03-23

Peptides

4-O-beta-D-mannosyl-D-glucose phosphorylase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

4-O-beta-D-mannosyl-D-glucose phosphorylase

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