MolNFT v1 · #134849 · protein
Complex of SETD8 with MS453
5TH7 · N-lysine methyltransferase KMT5A: “Complex of SETD8 with MS453”. X-ray diffraction, 2 ligands (7BY, UNX), 2 pockets (best druggability 0.81). MolNFT v1 #134849 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5TH7
- Type
- protein
- Length
- 288 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase KMT5A
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NQR1
- Ligands
- 7BY, UNX
- Pockets
- 2 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-lysine methyltransferase KMT5A (EC 2.1.1.-, 2.1.1.43) | protein | 143 | 23% helix, 39% strand | Q9NQR1 |
| B | N-lysine methyltransferase KMT5A (EC 2.1.1.-, 2.1.1.43) | protein | 145 | 22% helix, 38% strand | Q9NQR1 |
Ligands and binding sites
- 7BY · N-(3-{[6,7-dimethoxy-2-(pyrrolidin-1-yl)quinazolin-4-yl]amino}propyl)propanamide · ligand · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 21 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
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 | 449 | 0.81 | 0.89 | 59 | 7BY, UNX, EDO |
| 2 | 89 | 0.36 | 0.75 | 16 | UNX |
Interfaces
1 interface between chains.
- A–B · 987 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 Q9NQR1
- Elsewhere: RCSB PDB 5TH7 · PDBe 5TH7 · UniProt Q9NQR1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.