SMTL ID : 6g1b.1

Corynebacterium glutamicum OxyR, oxidized form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 2 residues within 4Å: Chain A: H.141 Chain B: H.141 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:H.141, B:H.141, H2O.3, H2O.10 NI.10: 2 residues within 4Å: Chain C: H.141 Chain D: H.141 4 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: D:H.141, C:H.141, H2O.14, H2O.22

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

FMT.2: 2 residues within 4Å: Chain A: Q.299, L.302 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.299 FMT.7: 6 residues within 4Å: Chain B: H.27, F.28, S.61, T.62, R.63, K.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.28 FMT.8: 3 residues within 4Å: Chain A: R.265 Chain B: T.264, R.265 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:W.261, A:R.265, B:R.265 Hydrogen bonds: B:T.264 FMT.11: 2 residues within 4Å: Chain C: Q.299, L.302 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.299 FMT.16: 6 residues within 4Å: Chain D: H.27, F.28, S.61, T.62, R.63, K.64 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:F.28 FMT.17: 3 residues within 4Å: Chain C: R.265 Chain D: T.264, R.265 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:R.265, C:W.261, C:R.265

2 x 1PS: 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE(Non-covalent)

1PS.3: 5 residues within 4Å: Chain A: K.166, S.289, S.290, S.291, S.292 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.166 1PS.12: 5 residues within 4Å: Chain C: K.166, S.289, S.290, S.291, S.292 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:K.166

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

NA.4: 3 residues within 4Å: Chain A: P.102, E.131, H.133 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.131, A:H.133 NA.13: 3 residues within 4Å: Chain C: P.102, E.131, H.133 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.131

6 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.5: 3 residues within 4Å: Chain A: D.137, H.141, L.145 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.137, B:R.234 PEO.6: 5 residues within 4Å: Chain A: K.166, E.167, I.168, Y.287, E.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.167 PEO.9: 3 residues within 4Å: Chain B: I.168, P.169, Q.305 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:P.169, B:Q.305, B:Q.305 PEO.14: 3 residues within 4Å: Chain C: D.137, H.141, L.145 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:D.137, D:R.234 PEO.15: 5 residues within 4Å: Chain C: K.166, E.167, I.168, Y.287, E.298 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.287, C:E.298 PEO.18: 3 residues within 4Å: Chain D: I.168, P.169, Q.305 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.305, D:Q.305

Links

RCSB   PDBe   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: AC
Hydrogen peroxide-inducible genes activator: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

C
J

B
B

D
B

Hydrogen peroxide-inducible genes activator

Hydrogen peroxide-inducible genes activator