MolNFT v1 · #142236 · protein

Catechol methyltransferase spcomt

5ZY6 · Probable catechol O-methyltransferase 1: “Catechol methyltransferase spcomt”. X-ray diffraction, 1 ligand (SAM), 4 pockets (best druggability 0.65). MolNFT v1 #142236 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5ZY6
Type: protein
Length: 485 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable catechol O-methyltransferase 1
EC: 2.1.1.6
UniProt: O42898
Ligands: SAM
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable catechol O-methyltransferase 1 (EC 2.1.1.6)	protein	240	47% helix, 18% strand	O42898
B	Probable catechol O-methyltransferase 1 (EC 2.1.1.6)	protein	245	46% helix, 18% strand	O42898

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

4 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	457	0.65	0.78	55	SAM
2	189	0.55	0.79	31	SAM
3	72	0.34	0.76	17	empty
4	59	0.30	0.75	13	empty

Interfaces

1 interface between chains.

A–B · 114 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5ZY6 · catechol methyltransferase spCOMT · the same entry in another collection · chain A against A, TM-score 1.00
O42898 · AlphaFold monomer V2.0 prediction for probable catechol O-methyltransferase 1 (O42898) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O42898
Elsewhere: RCSB PDB 5ZY6 · PDBe 5ZY6 · UniProt O42898

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