MolNFT v1 · #185108 · protein + DNA
Trinucleosome of the 4X197 nucleosome array containing H1
7PFA · Histone H3.2: “Trinucleosome of the 4X197 nucleosome array containing H1”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #185108 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7PFA
- Type
- protein + DNA
- Length
- 3,576 residues
- Chains
- 28
- 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; Histone H1.4; DNA…
- UniProt
- Q71DI3, P62805, P04908, O60814, P10412
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 7 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| K, O, A, E, a, e | Histone H3.2 | protein | 97 | 68% helix, 4% strand | Q71DI3 |
| L, P, B, F, b, f | Histone H4 | protein | 83 | 55% helix, 7% strand | P62805 |
| M, Q, C, G, c, g | Histone H2A type 1-B/E | protein | 109 | 50% helix, 6% strand | P04908 |
| N, R, D, H, d, h | Histone H2B type 1-K | protein | 95 | 72% helix, 4% strand | O60814 |
| U, u | Histone H1.4 | protein | 75 | 47% helix, 8% strand | P10412 |
| I | DNA (561-mer) | dna | 561 | — | — |
| J | DNA (561-mer) | dna | 561 | — | — |
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 | 1034 | 0.83 | 0.84 | 100 | empty |
| 2 | 687 | 0.79 | 0.84 | 71 | empty |
| 3 | 419 | 0.78 | 0.87 | 55 | empty |
| 4 | 662 | 0.78 | 0.83 | 79 | empty |
| 5 | 378 | 0.77 | 0.87 | 55 | empty |
Interfaces
115 interfaces between chains.
- I–J · 26936 Ų buried · 2,662 hydrogen bonds · nucleic-nucleic
- c–d · 2647 Ų buried · 30 hydrogen bonds · protein-protein
- G–H · 2646 Ų buried · 29 hydrogen bonds · protein-protein
- Q–R · 2630 Ų buried · 29 hydrogen bonds · protein-protein
- M–N · 2630 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 7PFA · Trinucleosome of the 4x197 nucleosome array containing H1 · the same entry in another collection · chain B against B, 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 Q71DI3
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt O60814
- Every structure of UniProt P10412
- Elsewhere: RCSB PDB 7PFA · PDBe 7PFA · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt O60814 · UniProt P10412
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