MolNFT v1 · #31446 · protein

Crystal structure of human catechol-O-methyltransferase domain containing 1

2AVD: “Crystal structure of human catechol-O-methyltransferase domain containing 1”. X-ray diffraction, 1 ligand (SAM), 5 pockets (best druggability 0.61). MolNFT v1 #31446 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2AVD
Type: protein
Length: 438 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Catechol-O-methyltransferase
UniProt: Q86VU5
Ligands: SAM
Pockets: 5 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Catechol-O-methyltransferase	protein	219	44% helix, 20% strand	Q86VU5

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	409	0.61	0.76	49	SAM
2	249	0.56	0.78	27	empty
3	131	0.53	0.81	20	empty
4	136	0.51	0.80	18	empty
5	138	0.48	0.78	26	SAM

Interfaces

1 interface between chains.

A–B · 2204 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

2AVD · Crystal Structure of Human Catechol-O-methyltransferase domain containing 1 · the same entry in another collection · chain A against A, TM-score 1.00
Q86VU5 · AlphaFold monomer V2.0 prediction for catechol O-methyltransferase domain-containing… · a predicted model of the same protein · 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 Q86VU5
Elsewhere: RCSB PDB 2AVD · PDBe 2AVD · UniProt Q86VU5

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