MolNFT v1 · #136322 · protein
Methyltransferase domain of human wolf-hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1)
5UPD · Histone-lysine N-methyltransferase NSD3: “Methyltransferase domain of human wolf-hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1)”. X-ray diffraction, 3 ligands (SAM, ZN, UNX), 3 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 5UPD
- Type
- protein
- Length
- 214 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase NSD3
- EC
- 2.1.1.43
- UniProt
- Q9BZ95
- Ligands
- SAM, ZN, UNX
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 13% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase NSD3 (EC 2.1.1.43) | protein | 214 | 13% helix, 28% strand | Q9BZ95 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- UNX · Unknown atom or ion · ion · 17 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 537 | 0.68 | 0.78 | 54 | SAM, UNX |
| 2 | 110 | 0.38 | 0.75 | 19 | UNX |
| 3 | 66 | 0.33 | 0.76 | 21 | UNX |
Compared structures
- 5UPD · Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BZ95 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase NSD3 (Q9BZ95) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9BZ95
- Elsewhere: RCSB PDB 5UPD · PDBe 5UPD · UniProt Q9BZ95
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