SMTL ID : 4tsl.1 (1 other biounit)

Crystal structure of FraC with POC bound (crystal form I)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x PC: PHOSPHOCHOLINE(Non-covalent)

PC.1: 13 residues within 4Å: Chain A: R.53, S.54, T.84, G.85, V.87, S.105, P.107, Y.108, Y.113, Y.133, Y.137, Y.138 Ligands: FMT.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.54, A:G.85, A:Y.108 Water bridges: A:A.83, A:D.109 pi-Cation interactions: A:Y.113 PC.2: 8 residues within 4Å: Chain A: W.112, Y.113, S.114, W.116, Y.137, Y.138, P.142 Ligands: FMT.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.112, A:S.114 Water bridges: A:W.112 pi-Cation interactions: A:W.116

5 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 4 residues within 4Å: Chain A: R.53, S.54, T.84 Ligands: PC.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.53, A:R.53, A:S.54 FMT.4: 2 residues within 4Å: Chain A: H.63, K.64 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.63 FMT.5: 5 residues within 4Å: Chain A: L.23, E.24, G.27, K.32, H.169 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.32 Water bridges: A:E.24, A:E.24, A:G.27 FMT.6: 5 residues within 4Å: Chain A: Y.113, S.114, W.116, Y.137 Ligands: PC.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.112, A:S.114 FMT.7: 3 residues within 4Å: Chain A: R.120, Y.122, K.123 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.120, A:R.120, A:K.123

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 5 residues within 4Å: Chain A: A.2, D.3, I.9, G.13, V.18 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.3, A:G.13

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.9: 4 residues within 4Å: Chain A: N.147, N.165, S.166, S.167 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.147, A:N.165, A:S.166, A:S.166, A:S.167

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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