SMTL ID : 6g1d.1

Corynebacterium glutamicum OxyR C206 mutant

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) EDO.2: 5 residues within 4Å: Chain A: L.192, R.219, D.275, V.276, T.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.219, A:T.277 EDO.3: 2 residues within 4Å: Chain A: Q.308, E.309 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.309 Water bridges: A:Q.308, A:A.312 EDO.8: 4 residues within 4Å: Chain B: P.259, W.260 Chain C: R.264, P.265 No protein-ligand interaction detected (PLIP) EDO.13: 8 residues within 4Å: Chain C: P.68, A.69, K.72 Chain D: A.94, N.95, G.96, S.97, E.295 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:K.72, D:A.94 Water bridges: D:E.295

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

FMT.4: 3 residues within 4Å: Chain A: L.45, E.49, I.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.49 FMT.11: 3 residues within 4Å: Chain C: H.26, F.27, G.28 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.27, C:G.28

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

SO4.5: 7 residues within 4Å: Chain A: I.107, P.108, T.109, T.138, H.207, S.208, L.209 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.109, A:T.138, A:S.208, A:S.208, A:L.209 Salt bridges: A:H.207 SO4.9: 7 residues within 4Å: Chain B: I.107, P.108, T.109, T.138, H.207, S.208, L.209 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.109, B:T.138, B:S.208, B:S.208, B:L.209 Water bridges: B:R.280 Salt bridges: B:H.207 SO4.12: 7 residues within 4Å: Chain C: I.107, P.108, T.109, T.138, H.207, S.208, L.209 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:T.109, C:T.109, C:T.109, C:S.208, C:L.209 Water bridges: C:R.280 Salt bridges: C:H.207 SO4.15: 7 residues within 4Å: Chain D: I.107, P.108, T.109, T.138, H.207, S.208, L.209 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.109, D:T.109, D:T.109, D:S.208, D:L.209 Water bridges: D:R.280 Salt bridges: D:H.207

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 6 residues within 4Å: Chain A: H.26, F.27, G.28, T.29, Q.38, V.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.27, A:G.28, A:T.29 PEG.7: 5 residues within 4Å: Chain A: P.259, W.260, L.313 Chain D: R.264, P.265 No protein-ligand interaction detected (PLIP) PEG.10: 7 residues within 4Å: Chain B: E.7, Y.8, R.9, P.10, T.11, Q.14, A.47 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.9, B:Q.14

1 x NA: SODIUM ION(Non-functional Binders)

NA.14: 2 residues within 4Å: Chain D: E.125, Y.126 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.125, D:Y.126

1 x FOR: FORMYL GROUP(Non-covalent)

FOR.16: 3 residues within 4Å: Chain D: L.169, Y.170, R.281 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pedre, B. et al., Structural snapshots of OxyR reveal the peroxidatic mechanism of H2O2sensing. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-12-05

Peptides

Hydrogen peroxide-inducible genes activator: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
B

D
A

Hydrogen peroxide-inducible genes activator