SMTL ID : 3fbz.5 (4 other biounits)

Crystal structure of ORF140 of the archaeal virus Acidianus Filamentous Virus 1 (AFV1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

8 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.1: 10 residues within 4Å: Chain A: L.29, I.30, P.31, E.32, M.34 Chain B: E.82, A.85, H.86 Chain D: N.25, G.27 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:E.32 Water bridges: A:E.32, A:D.33 Hydrophobic interactions: B:A.85, B:H.86 BOG.2: 13 residues within 4Å: Chain A: Y.49, M.53, E.82, A.85, H.86 Chain B: L.29, I.30, P.31, E.32, M.34 Chain C: N.25, G.27 Chain D: N.50 8 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: A:Y.49, A:E.82, A:A.85, A:H.86, B:P.31 Hydrogen bonds: C:N.25, B:E.32 Water bridges: B:D.33 BOG.3: 13 residues within 4Å: Chain A: D.45, Q.48, Y.49, W.89 Chain B: M.34, A.35, S.37, V.38, T.39 Chain C: I.30 Chain D: I.42, W.46 Ligands: BOG.7 8 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A, 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: B:A.35, B:V.38, B:T.39, A:Y.49, D:I.42, C:I.30 Hydrogen bonds: B:S.37, B:S.37 BOG.4: 14 residues within 4Å: Chain A: M.34, S.37, V.38 Chain B: I.42, D.45, W.46, Q.48, Y.49, W.89, N.93 Chain D: I.30, A.35, V.38 Ligands: BOG.8 8 PLIP interactions: 5 interactions with chain B, 2 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: B:I.42, B:W.46, B:Y.49, D:I.30, D:V.38 Hydrogen bonds: B:W.89, B:N.93, A:S.37 BOG.6: 13 residues within 4Å: Chain A: N.25, G.27 Chain C: Y.49, M.52, M.53, E.82, E.83, A.85, H.86 Chain D: L.29, I.30, P.31, M.34 8 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: A:G.27, C:E.83, D:L.29 Hydrophobic interactions: C:Y.49, C:A.85, C:H.86 Water bridges: C:E.83 Salt bridges: C:H.86 BOG.7: 11 residues within 4Å: Chain A: W.46 Chain B: I.30 Chain C: M.34, A.35, S.37, V.38, S.41 Chain D: D.45, W.89, N.93 Ligands: BOG.3 6 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:W.46, C:V.38, C:V.38, B:I.30 Hydrogen bonds: C:S.41, C:S.41 BOG.8: 15 residues within 4Å: Chain A: I.30, A.35, V.38 Chain C: I.42, D.45, W.46, Q.48, Y.49, M.52, W.89, N.93 Chain D: M.34, S.37, V.38 Ligands: BOG.4 9 PLIP interactions: 2 interactions with chain A, 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: A:I.30, A:V.38, C:I.42, C:W.46, C:Y.49, D:V.38 Hydrogen bonds: C:W.89, D:S.37, D:S.37 BOG.9: 12 residues within 4Å: Chain B: N.25, G.27 Chain C: L.29, I.30, P.31, M.34 Chain D: Y.49, M.53, E.82, E.83, A.85, H.86 12 PLIP interactions: 8 interactions with chain D, 2 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: D:Y.49, D:A.85, D:H.86 Hydrogen bonds: D:E.83, B:G.27, C:L.29 Water bridges: D:E.82, D:E.83, D:K.112, B:N.25, A:N.50 Salt bridges: D:H.86

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain B: R.15, Y.16, T.18, K.19 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain D: Y.16, T.18, K.19 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goulet, A. et al., Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage. Proc.Natl.Acad.Sci.USA (2009)

Release Date

2009-11-10

Peptides

Putative uncharacterized protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative uncharacterized protein

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