MolNFT v1 · #159389 · protein

Dehaloperoxidase B in complex with substtrate 4-nitro-cresol

6ONZ: “Dehaloperoxidase B in complex with substtrate 4-nitro-cresol”. X-ray diffraction, 3 ligands (HEM, MYJ, SO4), 2 pockets (best druggability 0.70). MolNFT v1 #159389 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ONZ
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, MYJ, SO4
Pockets: 2 · best druggability 0.70

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dehaloperoxidase B	protein	137	76% helix, 1% strand	Q9NAV7

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
MYJ · 2-methyl-4-nitrophenol · ligand · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 3 copies · chains A, B
EDO · 1,2-ethanediol · additive · 9 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	316	0.70	0.83	33	HEM, MYJ
2	288	0.70	0.83	30	HEM, MYJ

Interfaces

1 interface between chains.

A–B · 513 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6ONZ · Dehaloperoxidase B in complex with substtrate 4-nitro-cresol · 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 6ONZ · PDBe 6ONZ · UniProt Q9NAV7

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