MolNFT v1 · #138212 · protein
Crystal structure of the set domain of human SUV420H1 in complex with inhibitor
5WBV · Histone-lysine N-methyltransferase KMT5B: “Crystal structure of the set domain of human SUV420H1 in complex with inhibitor”. X-ray diffraction, 4 ligands (SAM, 9ZY, ZN), 3 pockets (best druggability 0.80). MolNFT v1 #138212 on…
- PDB
- 5WBV
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase KMT5B
- EC
- 2.1.1.43
- UniProt
- Q4FZB7
- Ligands
- SAM, 9ZY, ZN, UNX
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase KMT5B (EC 2.1.1.43) | protein | 233 | 36% helix, 22% strand | Q4FZB7 |
| B | Histone-lysine N-methyltransferase KMT5B (EC 2.1.1.43) | protein | 227 | 35% helix, 23% strand | Q4FZB7 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- 9ZY · 2-chloro-5-(4-methyl-6-oxo-3-phenylpyrano[2,3-c]pyrazol-1(6H)-yl)benzoic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.80 | 0.81 | 114 | 9ZY, UNX, SAM |
| 2 | 240 | 0.62 | 0.81 | 31 | SAM, UNX |
| 3 | 128 | 0.41 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 702 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5WBV · Crystal Structure of the SET Domain of Human SUV420H1 In Complex With Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q4FZB7 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase KMT5B (Q4FZB7) · 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 Q4FZB7
- Elsewhere: RCSB PDB 5WBV · PDBe 5WBV · UniProt Q4FZB7
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