Research workbench

Dehaloperoxidase B from amphitrite ornata: indazole complex

Analyse Dehaloperoxidase B from amphitrite ornata: indazole complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LK9
Type: protein
Length: 274 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dehaloperoxidase B
UniProt: Q9NAV7
Ligands: HEM, LZ1, SO4
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 77% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dehaloperoxidase B	protein	137	77% helix, 1% strand	Q9NAV7

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
LZ1 · 1H-indazole · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	363	0.72	0.83	28	HEM, LZ1
2	293	0.71	0.84	26	HEM, LZ1

Interfaces

1 interface between chains.

A–B · 511 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5LK9 · Dehaloperoxidase B from Amphitrite ornata: indazole complex · 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 Q9NAV7
Elsewhere: RCSB PDB 5LK9 · PDBe 5LK9 · UniProt Q9NAV7

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.