MolNFT v1 · #136842 · protein

Oxyferrous dehaloperoxidase B

5V5J: “Oxyferrous dehaloperoxidase B”. X-ray diffraction, 3 ligands (HEM, SO4, OXY), 3 pockets (best druggability 0.71). MolNFT v1 #136842 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V5J
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, SO4, OXY
Pockets: 3 · best druggability 0.71

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
SO4 · Sulfate ion · ion · 2 copies · chains A
OXY · Oxygen molecule · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 7 copies · chains A, B

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

Pockets

3 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	204	0.71	0.87	22	HEM, OXY
2	216	0.69	0.85	23	HEM, OXY
3	83	0.39	0.78	26	empty

Interfaces

1 interface between chains.

A–B · 489 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5V5J · oxyferrous Dehaloperoxidase B · 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 5V5J · PDBe 5V5J · UniProt Q9NAV7

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