MolNFT v1 · #69318 · protein

Crystal structure of VSET/SAH/H3 ternary complex

3KMT · A612L protein: “Crystal structure of VSET/SAH/H3 ternary complex”. X-ray diffraction, 1 ligand (SAH), 5 pockets (best druggability 0.54). MolNFT v1 #69318 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3KMT
Type: protein
Length: 381 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: A612L protein; Histone H3
UniProt: O41094, P68431
Ligands: SAH
Pockets: 5 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 9% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	A612L protein	protein	119	9% helix, 42% strand	O41094
G, H, I	Histone H3	protein	8	0% helix, 25% strand	P68431

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · 3 copies · chains A, G, B, H, C, I

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	206	0.54	0.78	27	SAH
2	237	0.54	0.77	26	empty
3	204	0.51	0.76	28	SAH
4	104	0.44	0.78	20	SAH
5	68	0.40	0.80	12	empty

Interfaces

5 interfaces between chains.

A–B · 1017 Å² buried · 8 hydrogen bonds · protein-protein
A–G · 698 Å² buried · 18 hydrogen bonds · protein-protein
C–I · 698 Å² buried · 18 hydrogen bonds · protein-protein
B–H · 688 Å² buried · 18 hydrogen bonds · protein-protein
A–C · 186 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 3 modified (methylation).

Compared structures

3KMT · Crystal structure of vSET/SAH/H3 ternary complex · the same entry in another collection · chain I against I, TM-score 1.00
P68431 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68431) · a predicted model of the same protein · chain I against A, TM-score 0.62

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 O41094
Every structure of UniProt P68431
Elsewhere: RCSB PDB 3KMT · PDBe 3KMT · UniProt O41094 · UniProt P68431

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