SMTL ID : 5m85.1

Three-dimensional structure of the intermediate state of GAF3 from Slr1393 of Synechocystis sp. PCC6803

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 22 residues within 4Å: Chain A: Y.74, F.84, Q.100, L.105, Q.107, D.108, T.109, Y.110, L.111, R.118, Y.119, L.125, T.136, C.138, H.139, N.142, F.151 Ligands: 3CX.2, NA.3, NA.5, NA.6, TRS.7 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.84, A:L.105, A:Y.110, A:Y.110, A:Y.110, A:L.111, A:H.139 Hydrogen bonds: A:D.108, A:D.108, A:T.109, A:Y.110 Water bridges: A:Y.74, A:F.84, A:D.108, A:T.109, A:T.109, A:T.153 Salt bridges: A:R.118, A:H.139 pi-Stacking: A:H.139

1 x 3CX: (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid(Non-covalent)

3CX.2: 6 residues within 4Å: Chain A: Y.110, R.118, A.133, G.134, F.135 Ligands: CYC.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.135 Hydrogen bonds: A:Y.110 Water bridges: A:R.118 Salt bridges: A:R.118

4 x NA: SODIUM ION(Non-functional Binders)

NA.3: 3 residues within 4Å: Chain A: Y.119, L.125 Ligands: CYC.1 No protein-ligand interaction detected (PLIP) NA.4: 3 residues within 4Å: Chain A: Y.197, Q.198, L.201 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.198 NA.5: 4 residues within 4Å: Chain A: F.135, T.136, H.139 Ligands: CYC.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.136, A:H.139 NA.6: 5 residues within 4Å: Chain A: D.108, T.109, Y.110, L.111 Ligands: CYC.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.108, A:Y.110, A:L.111 Water bridges: A:Q.112

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.7: 7 residues within 4Å: Chain A: F.84, H.139, L.143, F.146, I.148, Y.169 Ligands: CYC.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, X.-L. et al., Structural elements regulating the photochromicity in a cyanobacteriochrome. Proc.Natl.Acad.Sci.USA (2020)

Release Date

2017-12-20

Peptides

Sensory transduction histidine kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sensory transduction histidine kinase

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