SMTL ID : 4rq9.1

Crystal structure of the chromophore-binding domain of Stigmatella aurantiaca bacteriophytochrome (Thr289His mutant) in the Pr state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x BLA: BILIVERDINE IX ALPHA(Covalent)

BLA.1: 27 residues within 4Å: Chain A: C.38, E.41, I.43, I.195, Y.197, V.207, Y.219, F.224, S.227, D.228, I.229, P.230, A.233, Y.237, R.243, R.273, V.275, S.276, I.278, H.279, Y.282, M.286, S.291, S.293, L.305, S.307, H.309 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:I.195, A:V.207, A:Y.219, A:F.224, A:F.224, A:I.229, A:I.229, A:P.230, A:A.233, A:Y.237, A:I.278, A:H.279, A:Y.282, A:L.305 Hydrogen bonds: A:D.228, A:D.228, A:Y.237, A:S.276, A:H.279, A:S.291, A:S.307, A:S.307 Water bridges: A:I.43, A:R.273, A:M.292, A:M.292 Salt bridges: A:R.273, A:H.279 pi-Stacking: A:H.279 BLA.19: 27 residues within 4Å: Chain B: C.38, E.41, I.43, I.195, Y.197, V.207, Y.219, F.224, S.227, D.228, I.229, P.230, A.233, Y.237, R.243, R.273, V.275, S.276, I.278, H.279, Y.282, M.286, S.291, S.293, L.305, S.307, H.309 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:I.195, B:V.207, B:Y.219, B:F.224, B:F.224, B:I.229, B:I.229, B:P.230, B:A.233, B:Y.237, B:I.278, B:H.279, B:Y.282, B:L.305 Hydrogen bonds: B:D.228, B:D.228, B:S.276, B:S.291, B:S.307, B:S.307 Water bridges: B:I.43, B:R.273, B:M.292, B:M.292 Salt bridges: B:R.273, B:H.279 pi-Stacking: B:H.279

2 x SRT: S,R MESO-TARTARIC ACID(Non-covalent)

SRT.2: 5 residues within 4Å: Chain A: Q.183, R.186, A.211, R.212 Ligands: GOL.14 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.183, A:Q.183, A:R.186, A:R.212, A:R.212 Water bridges: A:Q.183 Salt bridges: A:R.186 SRT.20: 5 residues within 4Å: Chain B: Q.183, R.186, A.211, R.212 Ligands: GOL.32 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.183, B:Q.183, B:R.186, B:R.212, B:R.212 Water bridges: B:Q.183 Salt bridges: B:R.186

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: R.162, D.163, S.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.163 Water bridges: A:R.162 EDO.21: 3 residues within 4Å: Chain B: R.162, D.163, S.166 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.163, B:D.163 Water bridges: B:R.162, A:E.330

30 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: W.203, R.231, R.234, Q.238 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: I.248, D.249, L.280, E.281, H.284 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: G.187, L.188, T.189, G.190, R.315 Ligands: GOL.14 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: S.166, R.169, D.170 Chain B: W.241, E.330 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: K.110, L.239, N.240, W.241 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: K.110, R.134, H.135, F.269 Ligands: GOL.16 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: H.44, H.135, Q.136, L.236, L.239, D.266, S.268 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: G.221, L.222, H.223 Ligand excluded by PLIP GOL.12: 2 residues within 4Å: Chain A: P.145, Y.316 Ligand excluded by PLIP GOL.13: 5 residues within 4Å: Chain A: R.167, Q.183, E.184, G.187, L.188 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: R.186, G.187, G.190 Ligands: SRT.2, GOL.6 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: D.129, S.147, F.154, E.320 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain A: R.134, H.135, Q.136, G.137 Ligands: GOL.9 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain A: G.89, H.90, R.97, E.101 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain A: G.47, R.254, V.255, G.262 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain B: W.203, R.231, R.234, Q.238 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: I.248, D.249, L.280, E.281, H.284 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain B: G.187, L.188, T.189, G.190, R.315 Ligands: GOL.32 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain A: W.241, E.330 Chain B: S.166, R.169, D.170 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain B: K.110, L.239, N.240, W.241 Ligand excluded by PLIP GOL.27: 5 residues within 4Å: Chain B: K.110, R.134, H.135, F.269 Ligands: GOL.34 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain B: H.44, H.135, Q.136, L.236, L.239, D.266, S.268 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain B: G.221, L.222, H.223 Ligand excluded by PLIP GOL.30: 2 residues within 4Å: Chain B: P.145, Y.316 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain B: R.167, Q.183, E.184, G.187, L.188 Ligand excluded by PLIP GOL.32: 5 residues within 4Å: Chain B: R.186, G.187, G.190 Ligands: SRT.20, GOL.24 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain B: D.129, S.147, F.154, E.320 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain B: R.134, H.135, Q.136, G.137 Ligands: GOL.27 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain B: G.89, H.90, R.97, E.101 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain B: G.47, R.254, V.255, G.262 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Woitowich, N.C. et al., Crystal structure of the chromophore-binding domain of Stigmatella aurantiaca bacteriophytochrome (Thr289His mutant) in the Pr state. To be Published

Release Date

2016-05-11

Peptides

Photoreceptor-histidine kinase BphP: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Photoreceptor-histidine kinase BphP