MolNFT v1 · #167192 · protein
SETD2 in complex with a H3-variant super-substrate peptide
6VDB · Histone-lysine N-methyltransferase SETD2: “SETD2 in complex with a H3-variant super-substrate peptide”. X-ray diffraction, 4 ligands (SAH, ZN, UNX), 2 pockets (best druggability 0.65). MolNFT v1 #167192 on GenesisL1: 3D structure…
- PDB
- 6VDB
- Type
- protein
- Length
- 256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD2; Ala-pro-arg-phe-gly-gly-val-met-arg-pro-asn-arg
- EC
- 2.1.1.-
- UniProt
- Q9BYW2
- Ligands
- SAH, ZN, UNX, SCN
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD2 (EC 2.1.1.-) | protein | 244 | 20% helix, 26% strand | Q9BYW2 |
| H | Ala-pro-arg-phe-gly-gly-val-met-arg-pro-asn-arg | protein | 12 | 0% helix, 25% strand | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- UNX · Unknown atom or ion · ion · 20 copies · chains A, H
- SCN · Thiocyanate ion · ion · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.65 | 0.85 | 31 | SAH |
| 2 | 107 | 0.44 | 0.78 | 21 | UNX |
Interfaces
1 interface between chains.
- A–H · 1036 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6VDB · SETD2 in complex with a H3-variant super-substrate peptide · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYW2 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETD2 (Q9BYW2) · 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 Q9BYW2
- Elsewhere: RCSB PDB 6VDB · PDBe 6VDB · UniProt Q9BYW2
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