SMTL ID : 2nu5.1

Crystal structure of a complex of griffithsin cocrystallized with N-acetylglucosamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

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

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

SO4.4: 2 residues within 4Å: Chain A: N.94, T.95 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:R.6 Hydrogen bonds: A:T.95, A:T.95 SO4.8: 3 residues within 4Å: Chain A: R.6 Chain B: N.94, T.95 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.94, B:T.95 Water bridges: A:R.6 Salt bridges: A:R.6 SO4.9: 3 residues within 4Å: Chain B: R.25, N.46, L.47 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.46, B:L.47 Water bridges: B:R.25, B:R.25 Salt bridges: B:R.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ziolkowska, N.E. et al., Crystallographic studies of the complexes of antiviral protein griffithsin with glucose and N-acetylglucosamine. Protein Sci. (2007)

Release Date

2007-08-07

Peptides

griffithsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

griffithsin

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