SMTL ID : 4tsp.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: G.27, N.28, R.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.28 Salt bridges: A:R.79 SO4.4: 6 residues within 4Å: Chain A: N.28, V.29, K.30, K.77, R.79, G.80 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.30, A:G.80, A:G.80 Salt bridges: A:K.30, A:K.77, A:R.79

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

HXG.2: 16 residues within 4Å: Chain A: R.53, S.54, A.83, 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, PO4.6 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.84, A:Y.113 Hydrogen bonds: A:S.54, A:G.85, A:Y.108 Water bridges: A:D.109 pi-Cation interactions: A:Y.113 HXG.3: 8 residues within 4Å: Chain A: W.112, Y.113, W.116, Y.137, Y.138, P.142 Ligands: HXG.2, PO4.9 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.112 Hydrogen bonds: A:Y.137 pi-Cation interactions: A:W.116

5 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 5 residues within 4Å: Chain A: R.120, V.121, Y.122, K.123, Y.156 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.123, A:Y.156 Salt bridges: A:R.120 PO4.6: 6 residues within 4Å: Chain A: R.53, Q.130, Y.133, E.134, Y.138 Ligands: HXG.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.133, A:E.134, A:E.134, A:Y.138 Salt bridges: A:R.53 PO4.7: 2 residues within 4Å: Chain A: K.30, R.31 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.30 Salt bridges: A:R.31 PO4.8: 1 residues within 4Å: Chain A: H.169 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.32, A:H.169 PO4.9: 4 residues within 4Å: Chain A: S.114, W.116, R.144 Ligands: HXG.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.114, A:W.116 Salt bridges: A:R.144

1 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.10: 3 residues within 4Å: Chain A: F.16, K.20, E.24 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.20

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
B

Fragaceatoxin C

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