MolNFT v1 · #116926 · protein
Crystal structure of human PRMT8 in complex with sah
5DST · Protein arginine N-methyltransferase 8: “Crystal structure of human PRMT8 in complex with sah”. X-ray diffraction, 1 ligand (SAH), 20 pockets (best druggability 0.72). MolNFT v1 #116926 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DST
- Type
- protein
- Length
- 4,744 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein arginine N-methyltransferase 8
- EC
- 2.1.1.-
- UniProt
- Q9NR22
- Ligands
- SAH
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, G, J, K, L, M, N, O | Protein arginine N-methyltransferase 8 (EC 2.1.1.-) | protein | 316 | 26% helix, 39% strand | Q9NR22 |
| C, F, H, I | Protein arginine N-methyltransferase 8 (EC 2.1.1.-) | protein | 317 | 26% helix, 38% strand | Q9NR22 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 15 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.72 | 0.88 | 32 | SAH |
| 2 | 223 | 0.71 | 0.87 | 31 | SAH |
| 3 | 232 | 0.70 | 0.86 | 33 | SAH |
| 4 | 279 | 0.70 | 0.85 | 39 | SAH |
| 5 | 282 | 0.70 | 0.85 | 39 | SAH |
Interfaces
32 interfaces between chains.
- A–B · 1739 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1734 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1726 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 1723 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1719 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5DST · Crystal structure of human PRMT8 in complex with SAH · the same entry in another collection · chain J against J, TM-score 1.00
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 Q9NR22
- Elsewhere: RCSB PDB 5DST · PDBe 5DST · UniProt Q9NR22
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