MolNFT v1 · #156669 · protein

SETD3, a histidine methyltransferase, in complex with an actin peptide and sah, second P212121 crystal form

6MBL: “SETD3, a histidine methyltransferase, in complex with an actin peptide and sah, second P212121 crystal form”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.65). MolNFT v1 #156669 on GenesisL1: 3D structure…

PDB: 6MBL
Type: protein
Length: 496 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin peptide; Histone-lysine N-methyltransferase SETD3
EC: 2.1.1.43
UniProt: P60709, Q86TU7
Ligands: SAH
Pockets: 5 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Y	Actin peptide	protein	15	0% helix, 7% strand	P60709
A	Histone-lysine N-methyltransferase SETD3 (EC 2.1.1.43)	protein	481	51% helix, 12% strand	Q86TU7

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains Y, A
EDO · 1,2-ethanediol · additive · 10 copies · chains A, Y

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	342	0.65	0.80	32	SAH, EDO
2	165	0.56	0.81	34	empty
3	53	0.37	0.80	16	EDO
4	79	0.36	0.76	13	empty
5	50	0.31	0.76	14	EDO

Interfaces

1 interface between chains.

Y–A · 1094 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

6MBL · SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, Second… · the same entry in another collection · chain Y against Y, TM-score 1.00
Q86TU7 · AlphaFold monomer V2.0 prediction for actin-histidine N-methyltransferase (Q86TU7) · a predicted model of the same protein · chain A against A, TM-score 0.99
P60709 · AlphaFold monomer V2.0 prediction for actin, cytoplasmic 1 (P60709) · a predicted model of the same protein · chain Y against A, TM-score 0.23

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 P60709
Every structure of UniProt Q86TU7
Elsewhere: RCSB PDB 6MBL · PDBe 6MBL · UniProt P60709 · UniProt Q86TU7

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