SMTL ID : 3d6w.1

LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: N.70, I.72, D.88 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:I.72, H2O.1, H2O.1, H2O.2 MG.4: 3 residues within 4Å: Chain B: N.70, I.72, D.88 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:I.72, H2O.2, H2O.3, H2O.3 MG.7: 5 residues within 4Å: Chain A: P.15 Chain C: N.70, I.72, K.73, D.88 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:I.72, H2O.4, H2O.5, H2O.5 MG.9: 5 residues within 4Å: Chain B: P.15 Chain D: N.70, I.72, K.73, D.88 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:I.72, H2O.5, H2O.6, H2O.6

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

EDO.2: 6 residues within 4Å: Chain A: K.2, S.3, V.4 Chain C: K.55, D.56, L.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.3, A:V.4 EDO.5: 6 residues within 4Å: Chain B: K.2, S.3, V.4 Chain D: K.55, D.56, L.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.3, B:V.4

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

FMT.3: 5 residues within 4Å: Chain A: H.62, R.63, S.96, S.98, Y.99 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.63, A:S.96 Water bridges: A:S.98 FMT.6: 5 residues within 4Å: Chain B: H.62, R.63, S.96, S.98, Y.99 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.63, B:S.96 Water bridges: B:S.98 FMT.8: 5 residues within 4Å: Chain B: Y.76 Chain C: T.9, D.11, G.12, W.13 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:Y.76, C:D.11 FMT.10: 5 residues within 4Å: Chain A: Y.76 Chain D: T.9, D.11, G.12, W.13 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.9, D:D.11, D:D.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

OSIPIUK, J. et al., X-ray crystal structure of LytTr DNA-binding domain of putative methyl-accepting/DNA response regulator from Bacillus cereus. To be Published

Release Date

2008-07-15

Peptides

Methyl-accepting/DNA response regulator: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
B

D
B

Methyl-accepting/DNA response regulator