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

Analyse Crystal structure of SeMet-phytochromobilin synthase from tomato in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6KMD
Type: protein
Length: 281 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Solanum lycopersicum
Molecule: Phytochromobilin synthase
EC: 1.3.7.4
UniProt: Q588D6
Ligands: BLA, MG, CL
Pockets: 1 · best druggability 0.76

Structure

x-ray diffraction · resolution 2.2 · 1 distinct chain · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phytochromobilin synthase (EC 1.3.7.4)	protein	281	41% helix, 23% strand	Q588D6

Ligands and binding sites

BLA · Biliverdine IX alpha · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A
CL · Chloride ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	324	0.76	0.87	36	BLA

Modifications

Observed in the structure: 7 modified (engineered).

Compared structures

6KMD · Crystal structure of semet-phytochromobilin synthase from tomato in complex with… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q588D6
Elsewhere: RCSB PDB 6KMD · PDBe 6KMD · UniProt Q588D6

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