MolNFT v1 · #121262 · protein + DNA
Structural model of SET8 histone H4 LYS20 methyltransferase bound to nucleosome core particle
5HQ2 · Histone H3.2: “Structural model of SET8 histone H4 LYS20 methyltransferase bound to nucleosome core particle”. X-ray diffraction, 16 pockets (best druggability 0.83). MolNFT v1 #121262 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HQ2
- Type
- protein + DNA
- Length
- 1,104 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (149-mer); Guanine nucleotide…
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- P84233, P62799, Q6AZJ8, P02281, P21827, Q9NQR1
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 8 distinct chains · 29% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 99 | 64% helix, 3% strand | P84233 |
| B | Histone H4 | protein | 78 | 58% helix, 6% strand | P62799 |
| G | Histone H2A | protein | 105 | 53% helix, 3% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 95 | 68% helix, 1% strand | P02281 |
| I | DNA (149-mer) | dna | 73 | — | — |
| J | DNA (149-mer) | dna | 72 | — | — |
| K | Guanine nucleotide exchange factor SRM1 | protein | 422 | 4% helix, 22% strand | P21827 |
| M | N-lysine methyltransferase SETD8 (EC 2.1.1.-, 2.1.1.43) | protein | 160 | 22% helix, 23% strand | Q9NQR1 |
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1036 | 0.83 | 0.84 | 135 | empty |
| 2 | 1023 | 0.80 | 0.82 | 120 | empty |
| 3 | 685 | 0.79 | 0.84 | 116 | empty |
| 4 | 645 | 0.78 | 0.84 | 99 | empty |
| 5 | 375 | 0.75 | 0.86 | 53 | empty |
Interfaces
17 interfaces between chains.
- I–J · 3269 Ų buried · 264 hydrogen bonds · nucleic-nucleic
- G–H · 1029 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 996 Ų buried · 6 hydrogen bonds · protein-protein
- A–I · 412 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–J · 368 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 5HQ2 · Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core… · the same entry in another collection · chain M against M, TM-score 1.00
- Q9NQR1 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase KMT5A (Q9NQR1) · a predicted model of the same protein · chain M against A, TM-score 0.98
- P21827 · AlphaFold monomer V2.0 prediction for guanine nucleotide exchange factor SRM1 (P21827) · a predicted model of the same protein · chain K against A, TM-score 0.97
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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt P21827
- Every structure of UniProt Q9NQR1
- Elsewhere: RCSB PDB 5HQ2 · PDBe 5HQ2 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt P21827 · UniProt Q9NQR1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.