MolNFT v1 · #117077 · protein

Crystal structure of CARM1 and sinefungin

5DXJ · Histone-arginine methyltransferase CARM1: “Crystal structure of CARM1 and sinefungin”. X-ray diffraction, 1 ligand (SFG), 8 pockets (best druggability 0.85). MolNFT v1 #117077 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5DXJ
Type: protein
Length: 1,375 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histone-arginine methyltransferase CARM1
EC: 2.1.1.-, 2.1.1.125
UniProt: Q86X55
Ligands: SFG
Pockets: 8 · best druggability 0.85

Structure

x-ray diffraction · 2 distinct chains · 30% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Histone-arginine methyltransferase CARM1 (EC 2.1.1.-, 2.1.1.125)	protein	344	30% helix, 36% strand	Q86X55
C	Histone-arginine methyltransferase CARM1 (EC 2.1.1.-, 2.1.1.125)	protein	343	30% helix, 36% strand	Q86X55

Ligands and binding sites

SFG · Sinefungin · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 5 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	879	0.85	0.87	123	SFG, GOL
2	142	0.81	0.98	34	SFG
3	1077	0.81	0.82	101	SFG
4	248	0.62	0.81	29	empty
5	256	0.61	0.80	29	empty

Interfaces

5 interfaces between chains.

A–B · 1911 Å² buried · 25 hydrogen bonds · protein-protein
C–D · 1863 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 750 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 183 Å² buried · 1 hydrogen bond · protein-protein
A–D · 175 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5DXJ · Crystal structure of CARM1 and sinefungin · the same entry in another collection · chain A against A, TM-score 1.00
Q86X55 · AlphaFold monomer V2.0 prediction for histone-arginine methyltransferase CARM1 (Q86X55) · a predicted model of the same protein · chain B 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 Q86X55
Elsewhere: RCSB PDB 5DXJ · PDBe 5DXJ · UniProt Q86X55

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