SMTL ID : 2gud.1

Crystal structure of a complex of griffithsin with mannose at 0.94 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 0.94 Å

Oligo State

homo-dimer

Ligands

6 x MAN: alpha-D-mannopyranose(Non-covalent)(Non-functional Binders)

MAN.1: 8 residues within 4Å: Chain A: Y.69, G.109, D.110, Y.111, D.113 Chain B: G.12, G.13 Ligands: BMA.2 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.109, A:D.110, A:Y.111, B:G.13 Water bridges: A:D.110, A:D.110, B:G.13 MAN.3: 6 residues within 4Å: Chain A: G.27, S.28, Y.29, D.31, G.44, G.45 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.27, A:S.28, A:Y.29, A:Y.29, A:G.45 Water bridges: A:D.31, A:D.31 MAN.4: 7 residues within 4Å: Chain A: G.67, D.68, Y.69, D.71, G.90, G.91 Ligands: BMA.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.67, A:D.68, A:D.68, A:Y.69, A:G.91 MAN.7: 7 residues within 4Å: Chain A: G.12, G.13 Chain B: Y.69, G.109, D.110, Y.111, D.113 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.109, B:D.110, B:Y.111, B:Y.111, A:G.13 Water bridges: B:A.108, A:G.12 MAN.8: 6 residues within 4Å: Chain B: G.27, S.28, Y.29, D.31, G.44, G.45 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.27, B:S.28, B:S.28, B:Y.29, B:Y.29, B:G.45 Water bridges: B:N.46 MAN.9: 7 residues within 4Å: Chain B: Y.29, G.67, D.68, Y.69, D.71, G.90, G.91 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.67, B:D.68, B:Y.69, B:Y.69, B:G.91 Water bridges: B:D.68, B:G.90

2 x BMA: beta-D-mannopyranose(Non-covalent)

BMA.2: 8 residues within 4Å: Chain A: Y.69, G.109, D.110, Y.111, D.113 Chain B: G.12, G.13 Ligands: MAN.1 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.109, A:D.110, A:Y.111, B:G.13 Water bridges: A:D.110, A:D.113, A:D.113, B:G.12, B:G.13 BMA.5: 8 residues within 4Å: Chain A: Y.29, G.67, D.68, Y.69, D.71, G.90, G.91 Ligands: MAN.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.67, A:D.68, A:D.68, A:Y.69, A:G.91 Water bridges: A:G.90

1 x EDO: 1,2-ETHANEDIOL(Non-covalent)

EDO.6: 7 residues within 4Å: Chain A: N.61, M.62, T.63, S.74, F.75, E.76, T.95 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:M.62, A:T.63 Water bridges: A:N.61, A:S.74, A:S.74

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

SO4.10: 4 residues within 4Å: Chain B: R.65, G.91, S.92, A.93 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.93 Water bridges: B:R.65, B:R.65 Salt bridges: B:R.65

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Ziolkowska, N.E. et al., Domain-swapped structure of the potent antiviral protein griffithsin and its mode of carbohydrate binding. Structure (2006)

Release Date

2006-08-01

Peptides

griffithsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

griffithsin

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