SMTL ID : 5n0l.1

The structure of the cofactor binding GAF domain of the nutrient sensor CodY from Clostridium difficile

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

homo-hexamer

Ligands

6 x ILE: ISOLEUCINE(Non-covalent)

ILE.1: 11 residues within 4Å: Chain A: N.43, Y.45, D.63, S.65, F.77, Y.81, F.104, E.107, R.110, K.113, S.133 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:F.77, A:Y.81, A:F.104 Hydrogen bonds: A:N.43, A:Y.45, A:Y.45, A:D.63, A:R.110, A:S.133 Salt bridges: A:K.113 ILE.2: 12 residues within 4Å: Chain B: N.43, Y.45, D.63, S.65, F.77, F.104, E.107, R.110, K.113, T.115, V.131, S.133 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:Y.45, B:F.77, B:F.104, B:F.104, B:T.115, B:V.131 Hydrogen bonds: B:N.43, B:D.63, B:E.107, B:R.110, B:S.133 Salt bridges: B:K.113 ILE.3: 11 residues within 4Å: Chain C: N.43, Y.45, D.63, S.65, F.77, Y.81, E.107, R.110, K.113, V.131, S.133 11 PLIP interactions: 11 interactions with chain C, Hydrophobic interactions: C:Y.45, C:F.77, C:Y.81, C:V.131 Hydrogen bonds: C:N.43, C:Y.45, C:Y.45, C:D.63, C:R.110, C:S.133 Salt bridges: C:K.113 ILE.4: 12 residues within 4Å: Chain D: N.43, Y.45, D.63, S.65, F.77, Y.81, F.104, E.107, R.110, K.113, T.115, S.133 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:F.77, D:Y.81, D:F.104, D:F.104 Hydrogen bonds: D:N.43, D:Y.45, D:D.63, D:E.107, D:R.110, D:S.133 Salt bridges: D:K.113 ILE.5: 12 residues within 4Å: Chain E: N.43, Y.45, D.63, S.65, F.77, F.104, E.107, R.110, K.113, T.115, V.131, S.133 11 PLIP interactions: 11 interactions with chain E, Hydrophobic interactions: E:Y.45, E:F.77, E:F.104, E:F.104, E:T.115, E:V.131 Hydrogen bonds: E:N.43, E:Y.45, E:D.63, E:S.133 Salt bridges: E:K.113 ILE.6: 11 residues within 4Å: Chain F: N.43, Y.45, D.63, S.65, F.77, F.104, E.107, R.110, K.113, V.131, S.133 9 PLIP interactions: 9 interactions with chain F, Hydrophobic interactions: F:F.77, F:F.104, F:V.131 Hydrogen bonds: F:N.43, F:D.63, F:E.107, F:R.110, F:S.133 Salt bridges: F:K.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Daou, N. et al., Impact of CodY protein on metabolism, sporulation and virulence in Clostridioides difficile ribotype 027. Plos One (2019)

Release Date

2018-02-14

Peptides

GTP-sensing transcriptional pleiotropic repressor CodY: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

GTP-sensing transcriptional pleiotropic repressor CodY