SMTL ID : 3was.1

Crystal structure of 4-O-beta-D-mannosyl-D-glucose phosphorylase MGP complexed with Man-Glc+PO4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

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

BGC-BMA.1: 14 residues within 4Å: Chain A: N.73, R.88, R.94, Y.130, D.131, E.149, R.191, F.214, I.215, Y.284, V.319, F.324, D.344 Ligands: PO4.3 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:R.88, A:R.88, A:R.94, A:R.94, A:N.73, A:N.73, A:R.88, A:D.131, A:R.191 Water bridges: A:N.128, A:Y.130, C:H.248, C:R.276, C:R.276, C:R.276, A:Y.284, A:D.344 Salt bridges: A:R.94 BGC-BMA.2: 14 residues within 4Å: Chain B: N.73, R.88, R.94, Y.130, D.131, E.149, R.191, F.214, I.215, Y.284, V.319, F.324, D.344 Ligands: PO4.5 10 PLIP interactions: 3 interactions with chain F, 7 interactions with chain B Water bridges: F:R.276, F:R.276, F:R.276, B:N.128, B:Y.130, B:D.131, B:D.344 Hydrogen bonds: B:R.88, B:R.88, B:R.94, B:R.94, B:N.73, B:N.73, B:R.88, B:D.131, B:R.191 Salt bridges: B:R.94 BGC-BMA.7: 14 residues within 4Å: Chain C: N.73, R.88, R.94, Y.130, D.131, E.149, R.191, F.214, I.215, Y.284, V.319, F.324, D.344 Ligands: PO4.9 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain E Hydrogen bonds: C:R.88, C:R.88, C:R.94, C:R.94, C:N.73, C:N.73, C:R.88, C:D.131, C:R.191 Water bridges: C:N.128, C:Y.130, E:H.248, E:R.276, E:R.276, E:R.276, C:Y.284, C:D.344 Salt bridges: C:R.94 BGC-BMA.8: 14 residues within 4Å: Chain D: N.73, R.88, R.94, Y.130, D.131, E.149, R.191, F.214, I.215, Y.284, V.319, F.324, D.344 Ligands: PO4.11 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:R.88, D:R.88, D:R.94, D:R.94, D:N.73, D:N.73, D:R.88, D:D.131, D:R.191 Water bridges: D:N.128, B:H.248, B:R.276, B:R.276, B:R.276, D:D.131, D:D.344 Salt bridges: D:R.94 BGC-BMA.13: 14 residues within 4Å: Chain E: N.73, R.88, R.94, Y.130, D.131, E.149, R.191, F.214, I.215, Y.284, V.319, F.324, D.344 Ligands: PO4.15 12 PLIP interactions: 5 interactions with chain A, 7 interactions with chain E Water bridges: A:H.248, A:H.248, A:R.276, A:R.276, A:R.276, E:N.128, E:Y.284, E:D.344 Hydrogen bonds: E:R.88, E:R.88, E:R.94, E:R.94, E:N.73, E:N.73, E:R.88, E:D.131, E:R.191 Salt bridges: E:R.94 BGC-BMA.14: 14 residues within 4Å: Chain F: N.73, R.88, R.94, Y.130, D.131, E.149, R.191, F.214, I.215, Y.284, V.319, F.324, D.344 Ligands: PO4.17 11 PLIP interactions: 7 interactions with chain F, 4 interactions with chain D Hydrogen bonds: F:R.88, F:R.88, F:R.94, F:R.94, F:N.73, F:N.73, F:R.88, F:D.131, F:R.191 Water bridges: F:N.128, D:H.248, D:R.276, D:R.276, D:R.276, F:D.131, F:D.344 Salt bridges: F:R.94

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

PO4.3: 7 residues within 4Å: Chain A: R.191, N.192, R.209, K.254, H.273, Y.284 Ligands: BGC-BMA.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.192 Water bridges: A:K.254, A:Y.284 Salt bridges: A:R.191, A:R.209, A:K.254, A:H.273 PO4.4: 3 residues within 4Å: Chain A: V.311, G.312, R.315 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:G.312 Water bridges: A:P.310, A:R.315, E:R.346, E:R.346 Salt bridges: A:R.315 PO4.5: 7 residues within 4Å: Chain B: R.191, N.192, R.209, K.254, H.273, Y.284 Ligands: BGC-BMA.2 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.192, B:Y.284 Water bridges: B:K.254 Salt bridges: B:R.191, B:R.209, B:K.254, B:H.273 PO4.6: 3 residues within 4Å: Chain B: V.311, G.312, R.315 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain D Hydrogen bonds: B:G.312 Salt bridges: B:R.315 Water bridges: D:R.346, D:R.346, D:R.346, D:R.346 PO4.9: 7 residues within 4Å: Chain C: R.191, N.192, R.209, K.254, H.273, Y.284 Ligands: BGC-BMA.7 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:N.192 Water bridges: C:K.254, C:Y.284 Salt bridges: C:R.191, C:R.209, C:K.254, C:H.273 PO4.10: 3 residues within 4Å: Chain C: V.311, G.312, R.315 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:G.312 Water bridges: C:P.310, C:R.315, A:R.346, A:R.346 Salt bridges: C:R.315 PO4.11: 7 residues within 4Å: Chain D: R.191, N.192, R.209, K.254, H.273, Y.284 Ligands: BGC-BMA.8 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:N.192, D:Y.284 Water bridges: D:K.254 Salt bridges: D:R.191, D:R.209, D:K.254, D:H.273 PO4.12: 3 residues within 4Å: Chain D: V.311, G.312, R.315 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain F Hydrogen bonds: D:G.312 Salt bridges: D:R.315 Water bridges: F:R.346, F:R.346, F:R.346, F:R.346 PO4.15: 7 residues within 4Å: Chain E: R.191, N.192, R.209, K.254, H.273, Y.284 Ligands: BGC-BMA.13 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:N.192 Water bridges: E:K.254, E:Y.284 Salt bridges: E:R.191, E:R.209, E:K.254, E:H.273 PO4.16: 3 residues within 4Å: Chain E: V.311, G.312, R.315 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.312 Water bridges: E:P.310, E:R.315, C:R.346, C:R.346 Salt bridges: E:R.315 PO4.17: 7 residues within 4Å: Chain F: R.191, N.192, R.209, K.254, H.273, Y.284 Ligands: BGC-BMA.14 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:N.192, F:Y.284 Water bridges: F:K.254 Salt bridges: F:R.191, F:R.209, F:K.254, F:H.273 PO4.18: 3 residues within 4Å: Chain F: V.311, G.312, R.315 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain B Hydrogen bonds: F:G.312 Salt bridges: F:R.315 Water bridges: B:R.346, B:R.346, B:R.346, B:R.346

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakae, S. et al., Structure of Novel Enzyme in Mannan Biodegradation Process 4-O-beta-d-Mannosyl-d-Glucose Phosphorylase MGP. J.Mol.Biol. (2013)

Release Date

2013-09-04

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

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

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