SMTL ID : 7cuo.1

IclR transcription factor complexed with 4-hydroxybenzoic acid from Microbacterium hydrocarbonoxydans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: A.246, V.247, E.248 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.247, A:E.248 SO4.2: 5 residues within 4Å: Chain A: R.90, R.97 Chain B: E.39, N.42, R.154 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.42 Salt bridges: B:R.154, A:R.90, A:R.97 SO4.3: 5 residues within 4Å: Chain A: T.49, A.50, S.51, H.65, R.79 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.50, A:S.51 Water bridges: A:R.79 Salt bridges: A:H.65, A:R.79 SO4.5: 3 residues within 4Å: Chain B: A.246, V.247, E.248 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.247, B:E.248 SO4.6: 4 residues within 4Å: Chain B: H.169, Y.205, R.228, G.231 3 PLIP interactions: 3 interactions with chain B Water bridges: B:V.233 Salt bridges: B:H.169, B:R.228 SO4.7: 4 residues within 4Å: Chain A: Q.106 Chain B: R.138, R.150, V.151 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:V.151, A:Q.106 Water bridges: B:R.150, B:R.150 Salt bridges: B:R.138, B:R.150 SO4.8: 4 residues within 4Å: Chain B: T.49, A.50, S.51, H.65 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.49, B:A.50, B:S.51 Salt bridges: B:H.65 SO4.9: 6 residues within 4Å: Chain B: D.28, R.33, R.36, A.58, L.59, P.60 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.28 Salt bridges: B:R.33, B:R.36

2 x PHB: P-HYDROXYBENZOIC ACID(Non-covalent)

PHB.4: 10 residues within 4Å: Chain A: Q.124, N.147, L.148, L.155, S.160, S.161, S.162, I.216, G.222, V.240 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.155, A:I.216, A:I.216, A:V.240, A:V.240 Hydrogen bonds: A:N.147, A:L.148, A:S.161, A:S.162, A:G.222 PHB.10: 10 residues within 4Å: Chain B: Q.124, N.147, L.148, L.155, S.160, S.161, S.162, I.216, G.222, V.240 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.155, B:I.216, B:I.216, B:V.240, B:V.240 Hydrogen bonds: B:L.148, B:S.161, B:S.162, B:S.162, B:G.222 Water bridges: B:S.146, B:E.217

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akiyama, T. et al., Structural basis of the conformational changes in Microbacterium hydrocarbonoxydans IclR transcription factor homolog due to ligand binding. Biochim Biophys Acta Proteins Proteom (2021)

Release Date

2021-05-05

Peptides

Transcription factor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Transcription factor

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