SMTL ID : 5h20.1

X-ray structure of PadR-like Transcription factor from bacteroid fragilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

PO4.1: 2 residues within 4Å: Chain A: K.7, R.11 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.7, A:R.11 PO4.2: 2 residues within 4Å: Chain A: Y.29, Y.77 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.29 PO4.3: 4 residues within 4Å: Chain A: Y.29, S.31, D.32, R.75 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.31, A:D.32, A:D.32 Salt bridges: A:R.75 PO4.7: 2 residues within 4Å: Chain B: K.7, R.11 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.7, B:R.11 PO4.8: 2 residues within 4Å: Chain B: Y.29, Y.77 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.29, B:Y.29 PO4.9: 4 residues within 4Å: Chain B: Y.29, S.31, D.32, R.75 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.31, B:D.32, B:D.32 Salt bridges: B:R.75

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.4: 8 residues within 4Å: Chain A: Y.29, A.30, S.31, Y.50, P.74, R.75, K.76, Y.78 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.30, A:S.31, A:S.31, A:S.31, A:S.31, A:P.74, A:R.75, A:K.76 Salt bridges: A:R.75 GLC.10: 8 residues within 4Å: Chain B: Y.29, A.30, S.31, Y.50, P.74, R.75, K.76, Y.78 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:A.30, B:S.31, B:S.31, B:S.31, B:S.31, B:P.74, B:R.75, B:K.76 Salt bridges: B:R.75

4 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.5: 6 residues within 4Å: Chain A: R.11, M.14 Chain B: E.90, L.91, S.94 Ligands: IPA.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:R.11, A:R.11, A:M.14 Hydrogen bonds: B:E.90, B:S.94 IPA.6: 6 residues within 4Å: Chain A: M.14, L.15, C.18 Chain B: S.94, L.98 Ligands: IPA.5 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.14, A:L.15, B:L.98 IPA.11: 6 residues within 4Å: Chain A: E.90, L.91, S.94 Chain B: R.11, M.14 Ligands: IPA.12 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.90, A:E.90, A:S.94 Hydrophobic interactions: B:R.11, B:R.11, B:M.14 IPA.12: 6 residues within 4Å: Chain A: S.94, L.98 Chain B: M.14, L.15, C.18 Ligands: IPA.11 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.98, B:M.14, B:L.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, C. et al., Structural and functional analysis of BF2549, a PadR-like transcription factor from Bacteroides fragilis. Biochem. Biophys. Res. Commun. (2017)

Release Date

2017-03-08

Peptides

Putative PadR-family transcriptional regulatory protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative PadR-family transcriptional regulatory protein