SMTL ID : 6egu.1

Structure of RVFV envelope protein Gc in postfusion conformation in complex with 1,2-dipropionyl-sn-glycero-3-phosphocholine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

2 x NAG- FUL: beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUL.1: 3 residues within 4Å: Chain A: T.365, N.387, G.388 No protein-ligand interaction detected (PLIP) NAG-FUL.2: 2 residues within 4Å: Chain B: N.387, G.388 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.389 Hydrogen bonds: B:N.387

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.104 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.104 NAG.4: 5 residues within 4Å: Chain A: L.344, N.345, T.347, C.359, D.391 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.345, A:D.391 Water bridges: A:N.345, A:R.357 NAG.6: 2 residues within 4Å: Chain B: N.104, E.105 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain B: N.345, T.347, R.357, C.359, D.391 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.345, B:R.357, B:D.391, B:D.391 NAG.9: 1 residues within 4Å: Chain C: N.104 3 PLIP interactions: 3 interactions with chain C Water bridges: C:N.104, C:N.104, C:N.104 NAG.10: 5 residues within 4Å: Chain C: N.345, T.347, R.357, C.359, D.391 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.345, C:R.357, C:D.391

3 x 43Y: [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate(Non-covalent)

43Y.5: 9 residues within 4Å: Chain A: R.85, R.86, C.87, H.88, V.90, G.134, C.135, F.136, D.271 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.90 Hydrogen bonds: A:C.87, A:F.136 Salt bridges: A:R.86, A:D.271 43Y.8: 9 residues within 4Å: Chain B: R.85, R.86, C.87, V.90, G.134, C.135, F.136, N.137, D.271 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:V.90, B:F.136 Hydrogen bonds: B:C.87, B:F.136 Salt bridges: B:R.86, B:D.271 43Y.11: 8 residues within 4Å: Chain C: R.85, R.86, C.87, V.90, G.134, C.135, F.136, D.271 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:V.90, C:F.136 Hydrogen bonds: C:C.87, C:F.136 Water bridges: C:N.137 Salt bridges: C:R.86, C:D.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guardado-Calvo, P. et al., A glycerophospholipid-specific pocket in the RVFV class II fusion protein drives target membrane insertion. Science (2017)

Release Date

2017-11-01

Peptides

RVFV ENVELOPE PROTEIN GC: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

RVFV ENVELOPE PROTEIN GC

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