SMTL ID : 6kmd.1

Crystal structure of SeMet-phytochromobilin synthase from tomato in complex with biliverdin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x BLA: BILIVERDINE IX ALPHA(Non-covalent)

BLA.1: 23 residues within 4Å: Chain A: V.97, D.99, C.114, N.116, F.118, I.125, V.127, L.167, T.168, S.171, F.174, F.175, W.181, R.183, W.234, R.235, D.239, P.240, G.241, V.244, L.245, R.292, K.297 36 PLIP interactions: 36 interactions with chain A Hydrophobic interactions: A:V.97, A:D.99, A:N.116, A:F.118, A:F.118, A:I.125, A:I.125, A:V.127, A:V.127, A:L.167, A:F.174, A:F.175, A:W.181, A:W.181, A:R.235, A:P.240, A:P.240, A:V.244, A:V.244, A:V.244, A:L.245 Hydrogen bonds: A:N.116, A:T.168, A:T.168, A:S.171, A:S.171 Water bridges: A:G.241, A:R.292, A:K.297, A:K.297, A:K.297, A:K.297 Salt bridges: A:R.292, A:R.292, A:K.297, A:K.297

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: S.64, D.67 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.67, H2O.3, H2O.4, H2O.5 MG.3: 1 residues within 4Å: Chain A: E.43 No protein-ligand interaction detected (PLIP)

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

CL.4: 1 residues within 4Å: Chain A: R.183 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sugishima, M. et al., Crystal structure of phytochromobilin synthase in complex with biliverdin IX alpha , a key enzyme in the biosynthesis of phytochrome. J.Biol.Chem. (2020)

Release Date

2019-12-18

Peptides

Phytochromobilin synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Phytochromobilin synthase

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