SMTL ID : 6lxm.2 (1 other biounit)

Crystal structure of C-terminal DNA-binding domain of Escherichia coli OmpR as a domain-swapped dimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: K.36, A.37, S.40, H.41, L.54 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.37, A:S.40 Salt bridges: A:K.36, A:H.41 SO4.2: 4 residues within 4Å: Chain A: R.16, L.27, T.28, F.32 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.16, A:M.18, A:L.27, A:L.27 Salt bridges: A:R.16 SO4.8: 1 residues within 4Å: Chain B: W.92 No protein-ligand interaction detected (PLIP) SO4.9: 6 residues within 4Å: Chain B: R.75, A.83, P.85, Q.89, T.90, W.92 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.90, B:T.90 Water bridges: B:R.75, B:R.75, B:R.75 Salt bridges: B:R.75 SO4.10: 3 residues within 4Å: Chain B: S.66, V.69, R.73 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.73 Salt bridges: B:R.73

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: M.52, A.55, R.56, G.57, R.58, E.59, Y.60 Chain B: M.63 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:M.52, A:G.57, A:E.59, A:Y.60 Water bridges: A:R.58, B:M.63 GOL.4: 3 residues within 4Å: Chain A: L.27, T.28, S.29 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.27 GOL.5: 1 residues within 4Å: Chain A: R.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.16 GOL.6: 1 residues within 4Å: Chain A: R.73 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.73, A:R.73 Water bridges: A:Q.70 GOL.7: 1 residues within 4Å: Chain A: R.76 No protein-ligand interaction detected (PLIP) GOL.11: 6 residues within 4Å: Chain A: R.48 Chain B: D.68, W.92, G.93, G.95, Y.96 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.68, B:G.93, B:G.95 GOL.12: 4 residues within 4Å: Chain B: R.56, G.57, R.58, E.59 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.56, B:G.57, B:R.58, B:E.59 Water bridges: B:E.59

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sadotra, S. et al., Structural basis for promoter DNA recognition by the response regulator OmpR. J.Struct.Biol. (2020)

Release Date

2020-12-23

Peptides

Transcriptional regulatory protein OmpR: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transcriptional regulatory protein OmpR

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