SMTL ID : 2hyr.1

Crystal structure of a complex of griffithsin with maltose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

6 x BGC- GLC: alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose(Non-covalent)

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

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

SO4.7: 2 residues within 4Å: Chain A: N.94, T.95 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.94, A:T.95, A:T.95 Water bridges: A:A.93, B:R.6, B:R.6 SO4.8: 4 residues within 4Å: Chain A: R.65, G.91, S.92, A.93 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.91, A:A.93 Salt bridges: A:R.65 SO4.13: 4 residues within 4Å: Chain B: R.65, G.91, S.92, A.93 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.93, B:A.93 Salt bridges: B:R.65

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.11: 10 residues within 4Å: Chain A: G.18, L.19, I.35, D.36, Q.103 Chain B: G.18, L.19, I.35, D.36, Q.103 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.103, B:Q.103 EDO.12: 4 residues within 4Å: Chain A: T.50, F.51, T.52, R.81 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.52, A:T.52 EDO.14: 4 residues within 4Å: Chain B: S.60, N.61, T.77, N.78 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.60, B:N.61, B:N.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ziolkowska, N.E. et al., Crystallographic, thermodynamic, and molecular modeling studies of the mode of binding of oligosaccharides to the potent antiviral protein griffithsin. Proteins (2007)

Release Date

2007-04-24

Peptides

Griffithsin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Griffithsin

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