SMTL ID : 4p2v.1

Structure of the AI-2 processing enzyme LsrF in complex with the product of the LsrG reaction P-HPD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-10-mer

Ligands

10 x 26T: (3R)-3-hydroxy-2,4-dioxopentyl dihydrogen phosphate(Non-covalent)

26T.1: 13 residues within 4Å: Chain A: A.57, D.59, H.60, F.63, Q.143, Y.207, A.227, G.228, G.229, D.253, M.254, G.255, R.256 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.63 Hydrogen bonds: A:Y.207, A:G.228, A:G.229, A:G.255, A:R.256, A:R.256 Salt bridges: A:H.60, A:R.256 26T.2: 11 residues within 4Å: Chain B: A.57, D.59, H.60, Y.207, A.227, G.228, G.229, D.253, M.254, G.255, R.256 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.228, B:G.229, B:D.253, B:G.255, B:R.256 Salt bridges: B:H.60, B:R.256 26T.3: 12 residues within 4Å: Chain C: A.57, D.59, H.60, Q.143, Y.207, A.227, G.228, G.229, D.253, M.254, G.255, R.256 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:D.59, C:Y.207, C:Y.207, C:G.228, C:G.229, C:G.255, C:R.256 Water bridges: C:H.60, C:R.256 Salt bridges: C:H.60, C:R.256 26T.4: 12 residues within 4Å: Chain D: A.57, D.59, H.60, Y.62, F.63, Q.143, A.227, G.228, G.229, D.253, G.255, R.256 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.62, D:F.63 Hydrogen bonds: D:Q.143, D:G.228, D:G.229, D:R.256, D:R.256 Salt bridges: D:H.60, D:R.256 26T.5: 14 residues within 4Å: Chain E: A.57, D.59, H.60, F.63, Q.143, V.175, Y.207, A.227, G.228, G.229, D.253, M.254, G.255, R.256 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:V.175 Hydrogen bonds: E:G.228, E:G.229, E:D.253, E:G.255, E:R.256, E:R.256 Water bridges: E:Q.143, E:Y.207 Salt bridges: E:H.60, E:R.256 26T.6: 12 residues within 4Å: Chain F: D.59, H.60, Y.62, F.63, Q.143, A.227, G.228, G.229, D.253, M.254, G.255, R.256 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:F.63 Hydrogen bonds: F:D.59, F:G.228, F:G.229, F:G.255, F:R.256 Water bridges: F:N.257, F:N.257 Salt bridges: F:H.60, F:R.256 26T.7: 10 residues within 4Å: Chain G: A.57, H.60, Y.207, A.227, G.228, G.229, D.253, M.254, G.255, R.256 9 PLIP interactions: 9 interactions with chain G Hydrogen bonds: G:H.60, G:Y.207, G:G.228, G:G.229, G:G.255, G:R.256 Water bridges: G:Q.64 Salt bridges: G:H.60, G:R.256 26T.8: 13 residues within 4Å: Chain H: A.57, D.59, H.60, Q.143, V.175, Y.207, A.227, G.228, G.229, D.253, M.254, G.255, R.256 11 PLIP interactions: 11 interactions with chain H Hydrogen bonds: H:Y.207, H:Y.207, H:G.228, H:G.229, H:G.255, H:R.256 Water bridges: H:R.109, H:R.109, H:N.257 Salt bridges: H:H.60, H:R.256 26T.9: 11 residues within 4Å: Chain I: A.57, D.59, H.60, Y.62, R.109, A.227, G.228, G.229, D.253, G.255, R.256 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:Y.62 Hydrogen bonds: I:D.59, I:R.109, I:G.228, I:G.229, I:G.255, I:R.256 Salt bridges: I:H.60, I:R.256 26T.10: 11 residues within 4Å: Chain J: A.57, D.59, H.60, R.109, Q.143, G.228, G.229, D.253, M.254, G.255, R.256 10 PLIP interactions: 10 interactions with chain J Hydrogen bonds: J:R.109, J:Q.143, J:G.228, J:G.229, J:D.253, J:G.255, J:R.256 Water bridges: J:N.257 Salt bridges: J:H.60, J:R.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marques, J.C. et al., LsrF, a coenzyme A-dependent thiolase, catalyzes the terminal step in processing the quorum sensing signal autoinducer-2. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-09-17

Peptides

Uncharacterized aldolase LsrF: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
K

Uncharacterized aldolase LsrF