MolNFT v1 · #136850 · protein

Dehaloperoxidase a I9L mutant

5V5R: “Dehaloperoxidase a I9L mutant”. X-ray diffraction, 3 ligands (HEM, OXY, SO4), 3 pockets (best druggability 0.73). MolNFT v1 #136850 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V5R
Type: protein
Length: 274 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dehaloperoxidase a
UniProt: Q9NAV8
Ligands: HEM, OXY, SO4
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 76% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Dehaloperoxidase a	protein	137	76% helix, 1% strand	Q9NAV8

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains B, A
OXY · Oxygen molecule · ion · 2 copies · chains B, A
SO4 · Sulfate ion · ion · 2 copies · chains A
GOL · Glycerol · additive · chains 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	212	0.73	0.88	22	HEM, OXY
2	231	0.70	0.85	28	HEM, OXY
3	55	0.27	0.74	16	empty

Interfaces

1 interface between chains.

B–A · 503 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5V5R · Dehaloperoxidase A I9L mutant · the same entry in another collection · chain B against B, 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 Q9NAV8
Elsewhere: RCSB PDB 5V5R · PDBe 5V5R · UniProt Q9NAV8

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