SMTL ID : 4tsy.1

Crystal structure of FraC with lipids

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.14 Å

Oligo State

homo-octamer

Ligands

24 x HXJ: 2-[[(E,2S,3R)-2-(hexanoylamino)-3-oxidanyl-dec-4-enoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium(Non-covalent)

HXJ.1: 14 residues within 4Å: Chain A: R.53, S.54, A.83, T.84, G.85, V.87, S.105, P.107, Y.108, Y.113, Y.133, Y.137, Y.138 Ligands: SO4.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.54, A:A.83, A:G.85, A:Y.108, A:Y.113 pi-Cation interactions: A:Y.113 HXJ.2: 7 residues within 4Å: Chain A: N.111, W.112, Y.113, S.114, W.116, Y.137, P.142 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.112 Hydrogen bonds: A:W.112, A:S.114, A:Y.137 pi-Cation interactions: A:W.116 HXJ.10: 10 residues within 4Å: Chain A: V.29, R.31, Y.110, S.166, S.167, G.168 Chain B: T.56, N.78, R.79, P.81 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:R.31, A:R.31, A:G.168, B:R.79 pi-Cation interactions: A:Y.110 Hydrophobic interactions: B:P.81 Salt bridges: B:R.79 HXJ.11: 16 residues within 4Å: Chain B: 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: HXJ.12, SO4.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.83, B:Y.113 Hydrogen bonds: B:S.54, B:G.85, B:Y.108, B:Y.113 pi-Cation interactions: B:Y.113 HXJ.12: 8 residues within 4Å: Chain B: N.111, W.112, Y.113, W.116, Y.137, P.142 Ligands: HXJ.11, SO4.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:W.112, B:Y.137 pi-Cation interactions: B:W.116 HXJ.18: 9 residues within 4Å: Chain B: R.31, Y.110, S.166, S.167, G.168 Chain C: T.56, N.78, R.79, V.82 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:R.31, B:R.31, B:G.168, C:R.79 pi-Cation interactions: B:Y.110 Hydrophobic interactions: C:V.82 Salt bridges: C:R.79 HXJ.19: 17 residues within 4Å: Chain C: R.53, S.54, A.83, T.84, G.85, V.87, S.105, P.107, Y.108, D.109, W.112, Y.113, Y.133, Y.137, Y.138 Ligands: HXJ.20, SO4.23 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:S.54, C:G.85, C:Y.108, C:Y.113 pi-Cation interactions: C:Y.113 HXJ.20: 9 residues within 4Å: Chain C: N.111, W.112, Y.113, W.116, Y.137, Y.138, P.142 Ligands: HXJ.19, SO4.25 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:W.112, C:W.112 Hydrogen bonds: C:Y.137 pi-Cation interactions: C:W.116 HXJ.21: 11 residues within 4Å: Chain C: L.26, V.29, R.31, Y.110, S.166, S.167, G.168 Chain D: T.56, N.78, R.79, V.82 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.26 Hydrogen bonds: C:R.31, C:R.31, C:G.168, D:R.79 pi-Cation interactions: C:Y.110 Salt bridges: D:R.79 HXJ.26: 15 residues within 4Å: Chain D: 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: HXJ.27, SO4.30 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:S.54, D:A.83, D:G.85, D:Y.108, D:Y.113, D:Y.113 pi-Cation interactions: D:Y.113 HXJ.27: 9 residues within 4Å: Chain D: N.111, W.112, Y.113, W.116, Y.137, Y.138, P.142 Ligands: HXJ.26, SO4.32 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.112, D:W.112 pi-Cation interactions: D:W.116 HXJ.28: 11 residues within 4Å: Chain D: V.29, R.31, Y.110, S.166, S.167, G.168 Chain E: T.56, N.78, R.79, P.81, V.82 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain E Hydrogen bonds: D:R.31, D:R.31, D:G.168, E:R.79 pi-Cation interactions: D:Y.110 Hydrophobic interactions: E:P.81 Salt bridges: E:R.79 HXJ.33: 14 residues within 4Å: Chain E: R.53, S.54, A.83, T.84, G.85, V.87, S.105, P.107, Y.108, Y.113, Y.133, Y.137, Y.138 Ligands: SO4.36 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:S.54, E:A.83, E:G.85, E:Y.108, E:Y.113, E:Y.113 pi-Cation interactions: E:Y.113 HXJ.34: 7 residues within 4Å: Chain E: N.111, W.112, Y.113, S.114, W.116, Y.137, P.142 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:W.112 Hydrogen bonds: E:W.112, E:S.114 pi-Cation interactions: E:W.116 HXJ.42: 10 residues within 4Å: Chain E: V.29, R.31, Y.110, S.166, S.167, G.168 Chain F: T.56, N.78, R.79, P.81 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:P.81 Hydrogen bonds: F:R.79, E:R.31, E:R.31, E:G.168 Salt bridges: F:R.79 pi-Cation interactions: E:Y.110 HXJ.43: 16 residues within 4Å: Chain F: 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: HXJ.44, SO4.46 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:A.83, F:Y.113 Hydrogen bonds: F:S.54, F:G.85, F:Y.108, F:Y.113, F:Y.113 pi-Cation interactions: F:Y.113 HXJ.44: 8 residues within 4Å: Chain F: N.111, W.112, Y.113, W.116, Y.137, P.142 Ligands: HXJ.43, SO4.48 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:W.112 pi-Cation interactions: F:W.116 HXJ.50: 9 residues within 4Å: Chain F: R.31, Y.110, S.166, S.167, G.168 Chain G: T.56, N.78, R.79, V.82 7 PLIP interactions: 3 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:V.82 Hydrogen bonds: G:R.79, F:R.31, F:R.31, F:G.168 Salt bridges: G:R.79 pi-Cation interactions: F:Y.110 HXJ.51: 17 residues within 4Å: Chain G: R.53, S.54, A.83, T.84, G.85, V.87, S.105, P.107, Y.108, D.109, W.112, Y.113, Y.133, Y.137, Y.138 Ligands: HXJ.52, SO4.55 6 PLIP interactions: 6 interactions with chain G Hydrogen bonds: G:S.54, G:G.85, G:Y.108, G:Y.113, G:Y.113 pi-Cation interactions: G:Y.113 HXJ.52: 9 residues within 4Å: Chain G: N.111, W.112, Y.113, W.116, Y.137, Y.138, P.142 Ligands: HXJ.51, SO4.57 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:W.112, G:W.112 pi-Cation interactions: G:W.116 HXJ.53: 11 residues within 4Å: Chain G: L.26, V.29, R.31, Y.110, S.166, S.167, G.168 Chain H: T.56, N.78, R.79, V.82 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain H Hydrophobic interactions: G:L.26 Hydrogen bonds: G:R.31, G:R.31, G:G.168, H:R.79 pi-Cation interactions: G:Y.110 Salt bridges: H:R.79 HXJ.58: 15 residues within 4Å: Chain H: 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: HXJ.59, SO4.62 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:S.54, H:A.83, H:G.85, H:Y.108, H:Y.113 pi-Cation interactions: H:Y.113 HXJ.59: 9 residues within 4Å: Chain H: N.111, W.112, Y.113, W.116, Y.137, Y.138, P.142 Ligands: HXJ.58, SO4.64 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:W.112, H:W.112 Hydrogen bonds: H:Y.137 pi-Cation interactions: H:W.116 HXJ.60: 11 residues within 4Å: Chain A: T.56, N.78, R.79, P.81, V.82 Chain H: V.29, R.31, Y.110, S.166, S.167, G.168 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain H Hydrophobic interactions: A:P.81 Hydrogen bonds: A:R.79, H:R.31, H:R.31, H:G.168 Salt bridges: A:R.79 pi-Cation interactions: H:Y.110

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

SO4.3: 4 residues within 4Å: Chain A: R.120, V.121, Y.122, K.123 Ligand excluded by PLIP SO4.4: 5 residues within 4Å: Chain A: R.53, Q.130, Y.133, Y.138 Ligands: HXJ.1 Ligand excluded by PLIP SO4.5: 5 residues within 4Å: Chain A: W.149, R.161, E.173, H.175 Chain B: H.63 Ligand excluded by PLIP SO4.6: 5 residues within 4Å: Chain A: G.42, K.43, T.44, S.95 Ligands: HTO.9 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: R.79 Chain H: H.169 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain A: Y.51, F.52, R.53 Ligand excluded by PLIP SO4.13: 4 residues within 4Å: Chain B: R.120, V.121, Y.122, K.123 Ligand excluded by PLIP SO4.14: 5 residues within 4Å: Chain B: R.53, Q.130, Y.133, Y.138 Ligands: HXJ.11 Ligand excluded by PLIP SO4.15: 4 residues within 4Å: Chain B: R.161, E.173, H.175 Chain C: H.63 Ligand excluded by PLIP SO4.16: 5 residues within 4Å: Chain B: Y.113, S.114, W.116, R.144 Ligands: HXJ.12 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain B: W.149, H.150, S.151 Chain C: R.127 Ligand excluded by PLIP SO4.22: 5 residues within 4Å: Chain C: R.120, V.121, Y.122, K.123, Y.156 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain C: R.53, Q.130, Y.133, Y.138 Ligands: HXJ.19 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain C: R.161, E.173, H.175 Chain D: H.63, K.64 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: S.114, W.116, R.144 Ligands: HXJ.20 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain D: R.120, V.121, Y.122, K.123 Ligand excluded by PLIP SO4.30: 5 residues within 4Å: Chain D: R.53, Q.130, Y.133, Y.138 Ligands: HXJ.26 Ligand excluded by PLIP SO4.31: 4 residues within 4Å: Chain D: R.161, E.173, H.175 Chain E: H.63 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain D: W.112, S.114, W.116, R.144 Ligands: HXJ.27 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain E: R.120, V.121, Y.122, K.123 Ligand excluded by PLIP SO4.36: 5 residues within 4Å: Chain E: R.53, Q.130, Y.133, Y.138 Ligands: HXJ.33 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain E: W.149, R.161, E.173, H.175 Chain F: H.63 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain E: G.42, K.43, T.44, S.95 Ligands: HTO.41 Ligand excluded by PLIP SO4.39: 2 residues within 4Å: Chain D: H.169 Chain E: R.79 Ligand excluded by PLIP SO4.40: 3 residues within 4Å: Chain E: Y.51, F.52, R.53 Ligand excluded by PLIP SO4.45: 4 residues within 4Å: Chain F: R.120, V.121, Y.122, K.123 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain F: R.53, Q.130, Y.133, Y.138 Ligands: HXJ.43 Ligand excluded by PLIP SO4.47: 4 residues within 4Å: Chain F: R.161, E.173, H.175 Chain G: H.63 Ligand excluded by PLIP SO4.48: 5 residues within 4Å: Chain F: Y.113, S.114, W.116, R.144 Ligands: HXJ.44 Ligand excluded by PLIP SO4.49: 4 residues within 4Å: Chain F: W.149, H.150, S.151 Chain G: R.127 Ligand excluded by PLIP SO4.54: 5 residues within 4Å: Chain G: R.120, V.121, Y.122, K.123, Y.156 Ligand excluded by PLIP SO4.55: 5 residues within 4Å: Chain G: R.53, Q.130, Y.133, Y.138 Ligands: HXJ.51 Ligand excluded by PLIP SO4.56: 5 residues within 4Å: Chain G: R.161, E.173, H.175 Chain H: H.63, K.64 Ligand excluded by PLIP SO4.57: 4 residues within 4Å: Chain G: S.114, W.116, R.144 Ligands: HXJ.52 Ligand excluded by PLIP SO4.61: 4 residues within 4Å: Chain H: R.120, V.121, Y.122, K.123 Ligand excluded by PLIP SO4.62: 5 residues within 4Å: Chain H: R.53, Q.130, Y.133, Y.138 Ligands: HXJ.58 Ligand excluded by PLIP SO4.63: 4 residues within 4Å: Chain A: H.63 Chain H: R.161, E.173, H.175 Ligand excluded by PLIP SO4.64: 5 residues within 4Å: Chain H: W.112, S.114, W.116, R.144 Ligands: HXJ.59 Ligand excluded by PLIP

2 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)

HTO.9: 4 residues within 4Å: Chain A: K.43, S.95, D.96 Ligands: SO4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.43, A:S.95 HTO.41: 4 residues within 4Å: Chain E: K.43, S.95, D.96 Ligands: SO4.38 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.43, E:S.95

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: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Membrane

We predict this structure to be a membrane protein.
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Fragaceatoxin C

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