MolNFT v1 · #185112 · protein + DNA
Nucleosome 2 of the 4X197 nucleosome array containing H1
7PFE · Histone H3.2: “Nucleosome 2 of the 4X197 nucleosome array containing H1”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #185112 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7PFE
- Type
- protein + DNA
- Length
- 1,197 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 (177-mer)…
- UniProt
- Q71DI3, P62805, P04908, O60814, P10412
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 7 distinct chains · 61% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, e | Histone H3.2 | protein | 97 | 68% helix, 4% strand | Q71DI3 |
| b, f | Histone H4 | protein | 83 | 58% helix, 8% strand | P62805 |
| c, g | Histone H2A type 1-B/E | protein | 109 | 55% helix, 4% strand | P04908 |
| d, h | Histone H2B type 1-K | protein | 95 | 72% helix, 2% strand | O60814 |
| J | DNA (177-mer) | dna | 177 | — | — |
| I | DNA (177-mer) | dna | 177 | — | — |
| u | Histone H1.4 | protein | 75 | 49% helix, 12% strand | P10412 |
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 858 | 0.81 | 0.84 | 84 | empty |
| 2 | 352 | 0.77 | 0.88 | 48 | empty |
| 3 | 201 | 0.74 | 0.90 | 31 | empty |
| 4 | 364 | 0.73 | 0.85 | 38 | empty |
| 5 | 796 | 0.71 | 0.77 | 53 | empty |
Interfaces
38 interfaces between chains.
- J–I · 7953 Ų buried · 719 hydrogen bonds · nucleic-nucleic
- c–d · 2647 Ų buried · 30 hydrogen bonds · protein-protein
- g–h · 2560 Ų buried · 25 hydrogen bonds · protein-protein
- e–f · 2530 Ų buried · 23 hydrogen bonds · protein-protein
- a–b · 2495 Ų buried · 27 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 7PFE · PDBe 7PFE · UniProt Q71DI3 · UniProt P62805 · UniProt P04908 · UniProt O60814 · UniProt P10412
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