MolNFT v1 · #167207 · protein

Crystal structure of sfmd

6VDQ · 3-methyl-L-tyrosine peroxygenase: “Crystal structure of sfmd”. X-ray diffraction, 1 ligand (HEC), 5 pockets (best druggability 0.66). MolNFT v1 #167207 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VDQ
Type: protein
Length: 305 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-methyl-L-tyrosine peroxygenase
EC: 1.11.2.5
UniProt: B0CN28
Ligands: HEC
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 62% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-methyl-L-tyrosine peroxygenase (EC 1.11.2.5)	protein	305	62% helix, 3% strand	B0CN28

Ligands and binding sites

HEC · Heme C · ligand · chains A

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

Pockets

5 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	234	0.66	0.83	37	HEC
2	138	0.52	0.80	27	empty
3	102	0.42	0.78	19	empty
4	51	0.39	0.82	17	empty
5	64	0.37	0.79	17	empty

Modifications

Observed in the structure: 1 cofactor (heme c attachment).

Compared structures

6VDQ · Crystal structure of SfmD · the same entry in another collection · chain A against A, TM-score 1.00
B0CN28 · AlphaFold monomer V2.0 prediction for 3-methyl-L-tyrosine peroxygenase (B0CN28) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 B0CN28
Elsewhere: RCSB PDB 6VDQ · PDBe 6VDQ · UniProt B0CN28

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