MolNFT v1 · #125832 · protein

Dehaloperoxidase B from amphitrite ornata: imidazole complex

5LKV: “Dehaloperoxidase B from amphitrite ornata: imidazole complex”. X-ray diffraction, 2 ligands (HEM, SO4), 3 pockets (best druggability 0.69). MolNFT v1 #125832 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5LKV
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
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 75% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dehaloperoxidase B	protein	137	75% helix, 1% strand	Q9NAV7

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 4 copies · chains A, B
IMD · Imidazole · additive · 2 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

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	274	0.69	0.84	27	HEM, IMD
2	273	0.69	0.84	26	HEM, IMD
3	57	0.24	0.72	17	empty

Interfaces

1 interface between chains.

A–B · 501 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

5LKV · Dehaloperoxidase B from Amphitrite ornata: imidazole 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 5LKV · PDBe 5LKV · UniProt Q9NAV7

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