SMTL ID : 5aye.1

Crystal structure of Ruminococcus albus beta-(1,4)-mannooligosaccharide phosphorylase (RaMP2) in complexes with phosphate and beta-(1,4)-mannobiose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

6 x BMA- BMA: beta-D-mannopyranose-(1-4)-beta-D-mannopyranose(Non-covalent)

BMA-BMA.1: 13 residues within 4Å: Chain A: N.49, R.67, Y.114, D.115, R.162, G.185, H.186, Y.250, V.289, F.291, D.312 Chain C: C.245 Ligands: PO4.7 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.49, A:R.67, A:D.115, A:D.115, A:R.162, A:Y.250 Water bridges: A:N.49, A:H.186, A:K.220, A:D.312 BMA-BMA.2: 11 residues within 4Å: Chain A: C.245 Chain B: N.49, R.67, Y.114, D.115, R.162, H.186, Y.250, F.291, D.312 Ligands: PO4.8 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.49, B:R.67, B:D.115, B:R.162 Water bridges: B:H.186, B:K.220 BMA-BMA.3: 14 residues within 4Å: Chain B: C.245 Chain C: N.49, R.67, Y.114, D.115, R.162, N.163, G.185, H.186, Y.250, V.289, F.291, D.312 Ligands: PO4.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.49, C:R.67, C:D.115, C:D.115, C:R.162 Water bridges: C:H.186, C:K.220 BMA-BMA.4: 14 residues within 4Å: Chain D: N.49, R.67, Y.114, D.115, R.162, N.163, G.185, H.186, Y.250, V.289, F.291, D.312 Chain E: C.245 Ligands: PO4.10 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:N.49, D:R.67, D:D.115, D:R.162, D:Y.250 Water bridges: D:H.186 BMA-BMA.5: 14 residues within 4Å: Chain E: N.49, R.67, Y.114, D.115, R.162, G.185, H.186, Y.250, V.286, V.289, F.291, D.312 Chain F: C.245 Ligands: PO4.11 7 PLIP interactions: 1 interactions with chain F, 6 interactions with chain E Water bridges: F:C.245, E:D.115, E:H.186 Hydrogen bonds: E:N.49, E:R.67, E:D.115, E:R.162 BMA-BMA.6: 13 residues within 4Å: Chain D: C.245 Chain F: N.49, R.67, Y.114, D.115, R.162, N.163, H.186, Y.250, V.289, F.291, D.312 Ligands: PO4.12 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:N.49, F:R.67, F:D.115, F:R.162 Water bridges: F:H.186, F:K.220

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

PO4.7: 7 residues within 4Å: Chain A: R.162, N.163, R.180, K.220, H.239, Y.250 Ligands: BMA-BMA.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.163 Water bridges: A:K.220 Salt bridges: A:R.162, A:R.180, A:K.220, A:H.239 PO4.8: 7 residues within 4Å: Chain B: R.162, N.163, R.180, K.220, H.239, Y.250 Ligands: BMA-BMA.2 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.163, B:N.163, B:Y.250 Salt bridges: B:R.162, B:R.180, B:K.220, B:H.239 PO4.9: 7 residues within 4Å: Chain C: R.162, N.163, R.180, K.220, H.239, Y.250 Ligands: BMA-BMA.3 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.163, C:Y.250 Salt bridges: C:R.162, C:R.180, C:K.220, C:H.239 PO4.10: 7 residues within 4Å: Chain D: R.162, N.163, R.180, K.220, H.239, Y.250 Ligands: BMA-BMA.4 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:N.163 Salt bridges: D:R.162, D:R.180, D:K.220, D:H.239 PO4.11: 7 residues within 4Å: Chain E: R.162, N.163, R.180, K.220, H.239, Y.250 Ligands: BMA-BMA.5 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:N.163, E:Y.250 Salt bridges: E:R.162, E:R.180, E:K.220, E:H.239 PO4.12: 7 residues within 4Å: Chain F: R.162, N.163, R.180, K.220, H.239, Y.250 Ligands: BMA-BMA.6 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:N.163, F:N.163, F:Y.250 Water bridges: F:K.220 Salt bridges: F:R.162, F:R.180, F:K.220, F:H.239

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

Beta-1,4-mannooligosaccharide phosphorylase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Beta-1,4-mannooligosaccharide phosphorylase

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