SMTL ID : 8c7s.1

Transcriptional pleiotropic repressor CodY from Staphylococcus aureus in complex with Ile, GTP, and a 30-bp DNA fragment encompassing two overlapping binding sites

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

homo-tetramer

Ligands

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.1: 11 residues within 4Å: Chain C: V.22, D.23, F.24, S.43, R.44, R.45, K.47, L.49, I.154, E.157, K.158 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:V.22, C:V.22, C:V.22, C:F.24, C:S.43, C:R.44, C:R.45 Salt bridges: C:R.45, C:R.45, C:K.47, C:E.157, C:K.158 pi-Stacking: C:F.24 pi-Cation interactions: C:F.24 GTP.5: 12 residues within 4Å: Chain D: V.22, D.23, F.24, S.43, R.44, R.45, K.47, L.49, E.153, R.156, E.157, K.158 19 PLIP interactions: 19 interactions with chain D Hydrogen bonds: D:V.22, D:V.22, D:D.23, D:F.24, D:S.43, D:R.44, D:R.45, D:E.153, D:R.156, D:K.158, D:K.158 Salt bridges: D:R.44, D:R.45, D:K.47, D:E.157, D:K.158, D:K.158 pi-Stacking: D:F.24 pi-Cation interactions: D:F.24 GTP.8: 11 residues within 4Å: Chain G: V.22, D.23, F.24, S.43, R.44, R.45, K.47, L.49, I.154, E.157, K.158 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:V.22, G:V.22, G:V.22, G:D.23, G:F.24, G:S.43, G:R.44, G:R.45 Salt bridges: G:R.45, G:R.45, G:K.47, G:E.157, G:K.158 pi-Stacking: G:F.24 pi-Cation interactions: G:F.24 GTP.12: 12 residues within 4Å: Chain H: V.22, D.23, F.24, S.43, R.44, R.45, K.47, L.49, E.153, R.156, E.157, K.158 18 PLIP interactions: 18 interactions with chain H Hydrogen bonds: H:V.22, H:V.22, H:F.24, H:S.43, H:R.44, H:R.45, H:E.153, H:R.156, H:K.158, H:K.158 Salt bridges: H:R.44, H:R.45, H:K.47, H:E.157, H:K.158, H:K.158 pi-Stacking: H:F.24 pi-Cation interactions: H:F.24

4 x ILE: ISOLEUCINE(Non-covalent)

ILE.2: 9 residues within 4Å: Chain C: R.61, M.65, Y.75, V.94, T.96, V.97, F.98, P.99, P.100 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain C Hydrogen bonds: I.2, I.2, C:T.96 Salt bridges: C:R.61 ILE.6: 10 residues within 4Å: Chain D: R.61, M.65, P.72, Y.75, V.94, T.96, V.97, F.98, P.99, P.100 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:V.97 Hydrogen bonds: D:T.96, I.6, I.6 Salt bridges: D:R.61 ILE.9: 9 residues within 4Å: Chain G: R.61, M.65, Y.75, V.94, T.96, V.97, F.98, P.99, P.100 4 PLIP interactions: 2 Ligand-Ligand interactions, 2 interactions with chain G Hydrogen bonds: I.9, I.9, G:T.96 Salt bridges: G:R.61 ILE.13: 10 residues within 4Å: Chain H: R.61, M.65, P.72, Y.75, V.94, T.96, V.97, F.98, P.99, P.100 5 PLIP interactions: 2 Ligand-Ligand interactions, 3 interactions with chain H Hydrogen bonds: I.13, I.13, H:T.96 Hydrophobic interactions: H:V.97 Salt bridges: H:R.61

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

SO4.3: 4 residues within 4Å: Chain C: R.233, S.234 Chain E: T.18 Chain F: T.18 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.232, C:S.234 Salt bridges: C:R.233 SO4.4: 5 residues within 4Å: Chain C: K.164, R.167, D.168, K.246 Chain D: R.167 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:K.164, C:R.167, C:K.246 SO4.7: 4 residues within 4Å: Chain C: R.167 Chain D: K.164, R.167, D.168 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.168 Salt bridges: D:K.164, D:R.167 SO4.10: 4 residues within 4Å: Chain A: T.18 Chain B: T.18 Chain G: R.233, S.234 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.232, G:S.234 Salt bridges: G:R.233 SO4.11: 5 residues within 4Å: Chain G: K.164, R.167, D.168, K.246 Chain H: R.167 3 PLIP interactions: 3 interactions with chain G Salt bridges: G:K.164, G:R.167, G:K.246 SO4.14: 4 residues within 4Å: Chain G: R.167 Chain H: K.164, R.167, D.168 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:D.168 Salt bridges: H:K.164, H:R.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hainzl, T. et al., Structural insights into CodY activation and DNA recognition. Nucleic Acids Res. (2023)

Release Date

2023-07-19

Peptides

Global transcriptional regulator CodY (Fragment): CDGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

D
B

G
A

H
B

Global transcriptional regulator CodY (Fragment)