SMTL ID : 4tsq.1 (5 other biounits)

Crystal structure of FraC with DHPC bound (crystal form III)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

5 x HXG: 1,2-dihexanoyl-sn-glycero-3-phosphocholine(Non-covalent)

HXG.1: 14 residues within 4Å: Chain A: R.53, S.54, T.84, G.85, V.87, S.105, P.107, Y.108, W.112, Y.113, Y.133, Y.137, Y.138 Ligands: HXG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.112 Hydrogen bonds: A:S.54, A:G.85, A:Y.108 Water bridges: A:R.53, A:R.53, A:R.53, A:R.53, A:D.109 Salt bridges: A:R.53 pi-Cation interactions: A:Y.113 HXG.2: 7 residues within 4Å: Chain A: W.112, Y.113, W.116, Y.137, Y.138, P.142 Ligands: HXG.4 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.112 Hydrogen bonds: A:Y.113, A:Y.137 Water bridges: A:Y.138 pi-Cation interactions: A:W.116 HXG.3: 7 residues within 4Å: Chain A: R.53, Q.130, Y.133, E.134, Y.138 Ligands: HXG.1, PC.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.130, A:Y.133 Water bridges: A:R.53 Salt bridges: A:R.53, A:E.134 HXG.4: 8 residues within 4Å: Chain A: N.111, W.112, Y.113, S.114, W.116, R.144 Ligands: HXG.2, PC.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.116 Hydrogen bonds: A:S.114 Salt bridges: A:R.144 HXG.5: 8 residues within 4Å: Chain A: R.120, V.121, Y.122, K.123, R.140, L.154, G.155, Y.156 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:R.140 Hydrogen bonds: A:K.123 Water bridges: A:R.140 Salt bridges: A:R.140

2 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.6: 3 residues within 4Å: Chain A: N.78, V.82, T.84 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.84, A:T.84, A:T.84 Water bridges: A:N.78 PC.7: 4 residues within 4Å: Chain A: Y.138, H.139 Ligands: HXG.3, HXG.4 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.139

1 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.8: 6 residues within 4Å: Chain A: K.43, M.94, D.96, G.97, N.98, Y.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.96, A:N.98, A:N.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, K. et al., Structural basis for self-assembly of a cytolytic pore lined by protein and lipid. Nat Commun (2015)

Release Date

2015-03-04

Peptides

Fragaceatoxin C: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Fragaceatoxin C

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