MolNFT v1 · #185101 · protein + DNA
Nucleosome 4 of the 4X187 nucleosome array containing H1
7PF3 · Histone H3.2: “Nucleosome 4 of the 4X187 nucleosome array containing H1”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #185101 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7PF3
- Type
- protein + DNA
- Length
- 1,177 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-K; DNA (167-mer)…
- UniProt
- Q71DI3, P62805, P04908, O60814, P10412
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| k, o | Histone H3.2 | protein | 97 | 68% helix, 4% strand | Q71DI3 |
| l, p | Histone H4 | protein | 83 | 60% helix, 7% strand | P62805 |
| m, q | Histone H2A type 1-B/E | protein | 109 | 51% helix, 6% strand | P04908 |
| n, r | Histone H2B type 1-K | protein | 95 | 73% helix, 4% strand | O60814 |
| J | DNA (167-mer) | dna | 167 | — | — |
| I | DNA (167-mer) | dna | 167 | — | — |
| s | Histone H1.4 | protein | 75 | 49% helix, 12% strand | P10412 |
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 | 905 | 0.82 | 0.84 | 95 | empty |
| 2 | 370 | 0.77 | 0.87 | 37 | empty |
| 3 | 365 | 0.76 | 0.87 | 44 | empty |
| 4 | 209 | 0.72 | 0.89 | 29 | empty |
| 5 | 261 | 0.71 | 0.87 | 33 | empty |
Interfaces
38 interfaces between chains.
- J–I · 7497 Ų buried · 680 hydrogen bonds · nucleic-nucleic
- o–p · 2589 Ų buried · 25 hydrogen bonds · protein-protein
- m–n · 2560 Ų buried · 35 hydrogen bonds · protein-protein
- k–l · 2559 Ų buried · 25 hydrogen bonds · protein-protein
- q–r · 2558 Ų buried · 15 hydrogen bonds · protein-protein
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 Q71DI3
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt O60814
- Every structure of UniProt P10412
- Elsewhere: RCSB PDB 7PF3 · PDBe 7PF3 · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt O60814 · UniProt P10412
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