SMTL ID : 2gue.1

Crystal structure of a complex of griffithsin with N-acetylglucosamine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-dimer

Ligands

5 x SO4: SULFATE ION(Non-covalent)(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 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.69, A:G.109, A:D.110, A:Y.111, A:Y.111, B:G.13 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 SO4.17: 6 residues within 4Å: Chain A: G.13 Chain B: Y.69, G.109, D.110, Y.111, D.113 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.109, B:D.110, B:Y.111, A:G.13 SO4.18: 2 residues within 4Å: Chain B: K.100, Y.122 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.122 Water bridges: B:Y.122 Salt bridges: B:K.100 SO4.19: 1 residues within 4Å: Chain B: R.82 No protein-ligand interaction detected (PLIP)

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

EDO.3: 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 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: N.61, M.62, T.63, S.74, F.75, E.76, T.95 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: S.17, L.19, F.53, E.57, Y.58, I.59, V.101 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: N.105, D.116, Y.118 Ligands: EDO.7 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: N.105, G.106, S.107, S.114, D.116 Chain B: K.7, P.15, F.16 Ligands: EDO.6 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: A.23, L.47, S.48, P.49, T.50 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: F.51, T.52, G.54, E.57, R.81 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: S.26, G.27, P.85, Y.86, G.87 Ligands: EDO.13 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: L.47, S.48, P.49, Y.86 Ligands: EDO.13 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: N.94, T.95 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: V.24, S.26, N.46, L.47, S.48, Y.86 Ligands: EDO.10, EDO.11 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: F.16, S.17, L.19, S.20 Chain B: H.40 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: T.63, N.72, S.74, P.85 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: S.17, L.19, F.53, E.57, Y.58, I.59, V.101 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: S.66, G.67 Chain B: F.8, G.9 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain B: R.25, I.34, H.39, L.47 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain B: S.60, N.61, S.97, N.98 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain B: G.27, S.28, Y.29, D.31 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: T.63, R.65, N.72, I.73, S.74, P.85 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain A: F.16, K.100 Chain B: N.105, G.106, D.116, Y.118 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: R.25, G.45, N.46, L.47 Ligand excluded by PLIP

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-functional Binders)

NAG.16: 7 residues within 4Å: Chain B: Y.29, G.67, D.68, Y.69, D.71, G.90, G.91 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.68, B:D.68, B:D.68, B:Y.69, B:G.91

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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