SMTL ID : 5xbt.1

The structure of BrlR bound to c-di-GMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

4 x C2E: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)(Non-covalent)

C2E.1: 9 residues within 4Å: Chain A: S.2, M.3, R.33, G.35, S.36, D.37, N.38, Y.42 Chain B: Y.272 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.2, A:M.3, A:R.33, A:R.33, A:S.36, A:N.38, B:Y.272 Salt bridges: A:D.37 pi-Stacking: A:Y.42 C2E.2: 7 residues within 4Å: Chain A: P.63, E.65, A.66, R.69, R.72, F.85, R.88 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.69, A:R.88, A:R.88 Salt bridges: A:R.72 C2E.8: 9 residues within 4Å: Chain A: Y.272 Chain B: S.2, M.3, R.33, G.35, S.36, D.37, N.38, Y.42 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.3, B:R.33, B:R.33, B:S.36, B:D.37, B:N.38, B:Y.42 Salt bridges: B:D.37 pi-Stacking: B:Y.42 Water bridges: A:Y.272 C2E.9: 7 residues within 4Å: Chain B: P.63, E.65, A.66, R.69, R.72, F.85, R.88 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.69, B:R.88 Salt bridges: B:R.72

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.69, D.73, A.75, R.81, H.84, F.85, R.88 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.69, A:R.69, A:R.81, A:R.81, A:R.88 GOL.10: 7 residues within 4Å: Chain B: R.69, D.73, A.75, R.81, H.84, F.85, R.88 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.69, B:R.69, B:R.81, B:R.81, B:R.88, B:R.88 GOL.11: 4 residues within 4Å: Chain B: Y.139, S.142, A.143, P.144 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.139, B:Y.139

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

PEG.4: 6 residues within 4Å: Chain A: R.129, F.132, Y.172, E.190, Y.250, Y.268 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.129, A:E.190, A:Y.268 PEG.5: 4 residues within 4Å: Chain A: H.22, Y.23, R.58, L.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.22, A:R.58 PEG.6: 2 residues within 4Å: Chain A: H.116, H.233 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.233 PEG.12: 6 residues within 4Å: Chain B: R.129, F.132, Y.172, E.190, Y.250, Y.268 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.129, B:Y.172, B:E.190 PEG.13: 4 residues within 4Å: Chain B: T.19, H.22, Y.23, R.58 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.22, B:Y.23 PEG.14: 2 residues within 4Å: Chain B: H.116, H.233 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.233

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 4 residues within 4Å: Chain A: W.152, I.156, S.171, F.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.171 IMD.15: 4 residues within 4Å: Chain B: W.152, S.171, Y.251, F.255 1 PLIP interactions: 1 interactions with chain B pi-Stacking: B:W.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, F. et al., BrlR from Pseudomonas aeruginosa is a receptor for both cyclic di-GMP and pyocyanin. Nat Commun (2018)

Release Date

2018-05-02

Peptides

Probable transcriptional regulator: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Probable transcriptional regulator

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