SMTL ID : 2f8d.1

BenM effector-Binding domain crystallized from high pH conditions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

3 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.1: 7 residues within 4Å: Chain A: V.17, S.19, R.66, L.67, N.122, F.123, H.126 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:R.66, A:L.67, A:L.67, A:F.123, A:F.123, A:H.126 Hydrogen bonds: A:S.19 Salt bridges: A:R.66 BEZ.2: 10 residues within 4Å: Chain A: L.20, G.23, L.24, L.25, I.28, F.64, L.79, R.80, I.189, Y.213 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.20, A:L.25, A:L.25, A:I.28, A:F.64, A:L.79, A:I.189 Hydrogen bonds: A:L.24, A:Y.213 Salt bridges: A:R.80 BEZ.8: 10 residues within 4Å: Chain B: L.20, G.23, L.24, L.25, I.28, F.64, L.79, R.80, I.189, Y.213 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.20, B:L.20, B:L.24, B:L.25, B:I.28, B:F.64, B:L.79 Hydrogen bonds: B:L.24, B:Y.213, B:Y.213 Salt bridges: B:R.80

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: Y.44, M.46, R.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.59, A:R.59 GOL.4: 7 residues within 4Å: Chain A: K.75, T.77, Y.206, N.223, W.224, L.225, E.226 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:L.225, A:E.226 Water bridges: A:K.75, A:K.75, A:T.77, A:H.227 GOL.5: 5 residues within 4Å: Chain A: V.17, G.18, E.45, G.47, S.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.18, A:E.45, A:S.118 Water bridges: A:E.45 GOL.6: 6 residues within 4Å: Chain A: K.49, T.52, K.68, I.69, S.70, D.71 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.52, A:S.70, A:D.71 GOL.9: 8 residues within 4Å: Chain B: K.75, T.77, V.193, Y.206, N.223, W.224, L.225, E.226 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.223, B:L.225, B:E.226 Water bridges: B:K.75 GOL.10: 3 residues within 4Å: Chain B: Y.44, M.46, R.59 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.59, B:R.59, B:R.59

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.7: 1 residues within 4Å: Chain B: E.198 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ezezika, O.C. et al., Oligomerization of BenM, a LysR-type transcriptional regulator: structural basis for the aggregation of proteins in this family. Acta Crystallogr.,Sect.F (2007)

Release Date

2006-12-12

Peptides

HTH-type transcriptional regulator benM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HTH-type transcriptional regulator benM

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