MolNFT v1 · #36535 · protein + DNA
2.9 ångström X-ray structure of hybrid MACROH2A nucleosomes
2F8N · Alpha-satellite DNA (146 bp): “2.9 ångström X-ray structure of hybrid MACROH2A nucleosomes”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #36535 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2F8N
- Type
- protein + DNA
- Length
- 1,048 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-satellite DNA (146 bp); Histone H3.1; Histone H4; Histone 3, H2BA; Histone H2B.1…
- UniProt
- P84233, P62799, Q9D2U9, P02281, O75367, Q8CGP6
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 9 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Alpha-satellite DNA (146 bp) | dna | 145 | — | — |
| J | Alpha-satellite DNA (146 bp) | dna | 145 | — | — |
| A, E | Histone H3.1 | protein | 98 | 63% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 79 | 58% helix, 9% strand | P62799 |
| D | Histone 3, H2BA | protein | 93 | 73% helix, 4% strand | Q9D2U9 |
| F | Histone H4 | protein | 84 | 58% helix, 8% strand | P62799 |
| H | Histone H2B.1 | protein | 93 | 72% helix, 4% strand | P02281 |
| G | Core histone macro-H2A.1 | protein | 108 | 56% helix, 6% strand | O75367 |
| K | Histone H2A type 1 | protein | 105 | 57% helix, 7% strand | Q8CGP6 |
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 | 955 | 0.82 | 0.83 | 97 | empty |
| 2 | 720 | 0.78 | 0.83 | 56 | empty |
| 3 | 359 | 0.75 | 0.86 | 47 | empty |
| 4 | 221 | 0.68 | 0.86 | 32 | empty |
| 5 | 661 | 0.67 | 0.76 | 63 | empty |
Interfaces
35 interfaces between chains.
- I–J · 6253 Ų buried · 508 hydrogen bonds · nucleic-nucleic
- D–K · 2650 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2602 Ų buried · 26 hydrogen bonds · protein-protein
- H–G · 2568 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2498 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 2F8N · 2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes · the same entry in another collection · chain K against K, TM-score 1.00
- P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q8CGP6 · AlphaFold monomer V2.0 prediction for histone H2A type 1-H (Q8CGP6) · a predicted model of the same protein · chain K against A, TM-score 0.96
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 Q9D2U9
- Every structure of UniProt P02281
- Every structure of UniProt O75367
- Every structure of UniProt Q8CGP6
- Elsewhere: RCSB PDB 2F8N · PDBe 2F8N · UniProt P84233 · UniProt P62799 · UniProt Q9D2U9 · UniProt P02281 · UniProt O75367 · UniProt Q8CGP6
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