SMTL ID : 2gty.1

Crystal structure of unliganded griffithsin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 6 residues within 4Å: Chain A: Y.69, G.109, D.110, Y.111, D.113 Chain B: G.13 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.13, A:Y.69, A:G.109, A:D.110, A:Y.111 SO4.2: 2 residues within 4Å: Chain A: H.5, K.7 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.5, A:K.7 SO4.3: 6 residues within 4Å: Chain A: N.105, D.116, Y.118 Chain B: K.7, K.100 Ligands: SO4.10 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.105, A:D.116, A:Y.118, A:Y.118 Water bridges: A:G.106, A:G.106, A:G.106, B:K.100 Salt bridges: B:K.7, B:K.100 SO4.9: 6 residues within 4Å: Chain A: G.13 Chain B: Y.69, G.109, D.110, Y.111, D.113 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:G.13, B:G.109, B:D.110, B:Y.111 SO4.10: 2 residues within 4Å: Chain B: Y.122 Ligands: SO4.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.122 Water bridges: B:Y.122, B:Y.122 SO4.11: 5 residues within 4Å: Chain B: G.27, S.28, Y.29, D.31, G.45 7 PLIP interactions: 7 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, B:S.28 SO4.12: 3 residues within 4Å: Chain B: R.25, N.46, L.47 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.47 Water bridges: B:R.25, B:R.25 Salt bridges: B:R.25 SO4.13: 5 residues within 4Å: Chain B: G.67, D.68, Y.69, D.71, G.91 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.67, B:D.68, B:D.68, B:Y.69, B:D.71, B:G.91

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

EDO.4: 5 residues within 4Å: Chain A: G.27, S.28, Y.29, D.31, G.45 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.28, A:S.28, A:D.31 EDO.5: 6 residues within 4Å: Chain A: N.61, M.62, T.63, S.74, F.75, E.76 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.62, A:T.63 Water bridges: A:F.75, A:F.83 EDO.6: 7 residues within 4Å: Chain A: S.17, L.19, F.53, E.57, Y.58, I.59, V.101 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.17, A:S.17, A:I.59, A:V.101 EDO.7: 2 residues within 4Å: Chain A: Y.58, N.78 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.58, A:Y.58, A:N.78 EDO.8: 9 residues within 4Å: Chain A: G.18, L.19, 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.14: 5 residues within 4Å: Chain B: S.74, F.75, R.82, F.83, G.84 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.82, B:F.83, B:G.84

Links

RCSB   PDBe   PDBe-KB   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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