SMTL ID : 5i5l.1

The photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x BLA: BILIVERDINE IX ALPHA(Covalent)

BLA.1: 22 residues within 4Å: Chain A: C.11, I.16, L.155, Y.157, F.184, G.187, D.188, I.189, P.190, A.193, Y.197, R.235, V.237, S.238, V.240, H.241, Y.244, M.248, S.253, S.255, L.267, H.271 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:I.16, A:L.155, A:Y.157, A:F.184, A:F.184, A:F.184, A:D.188, A:I.189, A:I.189, A:P.190, A:A.193, A:Y.197, A:V.240, A:H.241, A:Y.244, A:L.267 Hydrogen bonds: A:D.188, A:D.188, A:Y.197, A:S.238, A:H.241, A:S.253, A:H.271 Salt bridges: A:R.235, A:H.241, A:H.271 pi-Cation interactions: A:H.241 BLA.5: 22 residues within 4Å: Chain B: C.11, I.16, L.155, Y.157, F.184, G.187, D.188, I.189, P.190, A.193, Y.197, R.235, V.237, S.238, V.240, H.241, Y.244, M.248, S.253, S.255, L.267, H.271 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:I.16, B:L.155, B:Y.157, B:F.184, B:F.184, B:F.184, B:D.188, B:I.189, B:I.189, B:P.190, B:A.193, B:Y.197, B:V.240, B:H.241, B:Y.244, B:L.267 Hydrogen bonds: B:D.188, B:D.188, B:D.188, B:S.238, B:Y.244, B:S.253, B:H.271 Salt bridges: B:R.235, B:H.241, B:H.271 pi-Cation interactions: B:H.241

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 2 residues within 4Å: Chain A: D.158, F.159 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:F.159, H2O.1, H2O.1, H2O.1, H2O.1 CA.6: 2 residues within 4Å: Chain B: D.158, F.159 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:F.159, H2O.2, H2O.2, H2O.2, H2O.2

2 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.3: 2 residues within 4Å: Chain A: Q.316, E.480 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.309, A:E.480 TAM.7: 2 residues within 4Å: Chain B: Q.316, E.480 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.309, B:E.480

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: D.152, R.153, E.170, G.172, S.173, G.174, L.176, P.177, S.178 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.170, A:E.170, A:L.176 GOL.8: 9 residues within 4Å: Chain B: D.152, R.153, E.170, G.172, S.173, G.174, L.176, P.177, S.178 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.170, B:L.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagano, S. et al., The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers. J.Biol.Chem. (2016)

Release Date

2016-08-03

Peptides

Bacteriophytochrome protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Bacteriophytochrome protein