SMTL ID : 2f97.1

Effector Binding Domain of BenM (crystals generated from high pH conditions)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: L.25, I.28, F.64, L.79, I.189, I.209, Y.213 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.28, A:F.64, A:L.79 Hydrogen bonds: A:L.25, A:Y.213, A:Y.213 Water bridges: A:L.24, A:L.24, A:R.80 ACT.6: 7 residues within 4Å: Chain B: L.25, I.28, F.64, L.79, I.189, I.209, Y.213 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.28, B:F.64, B:L.79 Hydrogen bonds: B:L.25, B:Y.213 Water bridges: B:L.24, B:L.24, B:R.80

4 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 9 residues within 4Å: Chain A: V.17, G.18, E.45, M.46, G.47, S.117, S.118, P.119 Chain B: R.145 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:G.18, A:E.45, A:S.118 Water bridges: A:E.45, A:E.45, B:R.145, B:R.145, B:R.145, B:R.145 PG4.3: 5 residues within 4Å: Chain A: R.13, Y.44, M.46, G.58, R.59 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.57, A:R.59 PG4.7: 9 residues within 4Å: Chain A: R.145 Chain B: V.17, G.18, E.45, M.46, G.47, S.117, S.118, P.119 8 PLIP interactions: 4 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.18, B:S.118 Water bridges: B:E.45, B:E.45, A:R.145, A:R.145, A:R.145, A:R.145 PG4.8: 5 residues within 4Å: Chain B: R.13, Y.44, M.46, G.58, R.59 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.57, B:R.59

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

PEG.4: 4 residues within 4Å: Chain A: H.36, T.200, Y.203, S.204 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.204 PEG.5: 10 residues within 4Å: Chain A: K.75, T.77, V.193, R.194, N.195, E.197, Y.206, P.222, N.223, W.224 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.75, A:T.77, A:N.195, A:N.223 PEG.9: 4 residues within 4Å: Chain B: H.36, T.200, Y.203, S.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.204 PEG.10: 10 residues within 4Å: Chain B: K.75, T.77, V.193, R.194, N.195, E.197, Y.206, P.222, N.223, W.224 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.75, B:N.195, B:N.223

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

2006-12-19

Peptides

HTH-type transcriptional regulator benM: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

HTH-type transcriptional regulator benM

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