Research workbench
Crystal structure of the set domain of human SUV420H1 in complex with inhibitor
Analyse Crystal structure of the set domain of human SUV420H1 in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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