Research workbench
Structural model of SET8 histone H4 LYS20 methyltransferase bound to nucleosome core particle
Analyse Structural model of SET8 histone H4 LYS20 methyltransferase bound to nucleosome… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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