SMTL ID : 5akp.1

Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP from Xanthomonas campestris bound to BV chromophore

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-dimer

Ligands

2 x BLA: BILIVERDINE IX ALPHA(Covalent)(Non-covalent)

BLA.1: 23 residues within 4Å: Chain A: C.19, I.24, M.172, I.184, Y.196, Y.201, S.204, D.205, I.206, P.207, A.210, Y.214, R.220, R.252, V.254, S.255, V.257, H.258, Y.261, T.270, V.272, S.286, H.288 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.184, A:Y.196, A:Y.201, A:Y.201, A:A.210, A:V.257, A:Y.261, A:T.270, A:V.272, A:V.272 Hydrogen bonds: A:D.205, A:Y.214, A:S.255, A:T.270, A:S.286, A:S.286 Water bridges: A:D.205, A:H.258 Salt bridges: A:R.220, A:R.252, A:H.258, A:H.288 pi-Stacking: A:Y.201 BLA.4: 24 residues within 4Å: Chain B: C.19, I.24, M.172, Y.174, I.184, Y.201, S.204, D.205, I.206, P.207, A.210, Y.214, R.220, R.252, V.254, S.255, V.257, H.258, Y.261, L.262, T.270, V.272, S.286, H.288 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:Y.174, B:I.184, B:Y.201, B:Y.201, B:Y.201, B:I.206, B:A.210, B:V.257, B:V.272, B:V.272 Hydrogen bonds: B:D.205, B:Y.214, B:S.255, B:T.270, B:S.286, B:S.286 Water bridges: B:D.205, B:H.258 Salt bridges: B:R.220, B:R.252, B:H.258, B:H.288 pi-Stacking: B:Y.201

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

TRS.2: 4 residues within 4Å: Chain A: D.177, E.178, W.180, L.281 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.180, A:W.180, A:L.281 TRS.5: 6 residues within 4Å: Chain B: F.176, D.177, E.178, W.180, L.281, W.282 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.177, B:L.281

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Chain A: D.245 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Otero, L.H. et al., Structure of the Full-Length Bacteriophytochrome from the Plant Pathogen Xanthomonas Campestris Provides Clues to its Long-Range Signaling Mechanism. J.Mol.Biol. (2016)

Release Date

2016-05-04

Peptides

PHYTOCHROME-LIKE PROTEIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PHYTOCHROME-LIKE PROTEIN

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