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Crystal structure of CARNMT1 bound to SAM

Analyse Crystal structure of CARNMT1 bound to SAM in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5YF0
Type: protein
Length: 687 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Carnosine N-methyltransferase
EC: 2.1.1.22
UniProt: Q8N4J0
Ligands: SAM, CA
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Carnosine N-methyltransferase (EC 2.1.1.22)	protein	336	48% helix, 20% strand	Q8N4J0
B	Carnosine N-methyltransferase (EC 2.1.1.22)	protein	351	48% helix, 19% strand	Q8N4J0

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains B
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
ACT · Acetate ion · additive · 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	861	0.77	0.81	75	ACT, SAM
2	914	0.77	0.80	78	ACT, SAM
3	81	0.56	0.86	25	EDO
4	64	0.52	0.86	23	EDO
5	122	0.42	0.76	30	empty

Interfaces

1 interface between chains.

A–B · 2476 Å² buried · 64 hydrogen bonds · protein-protein

Compared structures

5YF0 · Crystal structure of CARNMT1 bound to SAM · the same entry in another collection · chain B against B, TM-score 1.00
Q8N4J0 · AlphaFold monomer V2.0 prediction for carnosine N-methyltransferase (Q8N4J0) · 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 Q8N4J0
Elsewhere: RCSB PDB 5YF0 · PDBe 5YF0 · UniProt Q8N4J0

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