MolNFT v2 · #155818 · protein

Crystal structure of phytochromobilin synthase from tomato in complex with biliverdin

6KME: “Crystal structure of phytochromobilin synthase from tomato in complex with biliverdin”. X-ray diffraction at 1.95, 3 ligands (BLA, MG, CL), 2 pockets (best druggability 0.76). MolNFT v2 #155818 on GenesisL1: 3D structure, binding…

PDB: 6KME
Type: protein
Length: 284 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.95
Source: Solanum lycopersicum
Molecule: Phytochromobilin synthase
EC: 1.3.7.4
UniProt: Q588D6
Ligands: BLA, MG, CL
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · resolution 1.95 · 1 distinct chain · 41% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phytochromobilin synthase (EC 1.3.7.4)	protein	284	41% helix, 23% strand	Q588D6

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	325	0.76	0.87	36	BLA
2	50	0.25	0.73	16	empty

Compared structures

6KME · Crystal structure of phytochromobilin synthase from tomato in complex with biliverdin · 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 6KME · PDBe 6KME · UniProt Q588D6

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