MolNFT v1 · #175796 · protein + DNA
Cryo-EM structure of SET8-nucleosome complex
7D1Z · Histone H3.1: “Cryo-EM structure of SET8-nucleosome complex”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #175796 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7D1Z
- Type
- protein + DNA
- Length
- 1,219 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (145-mer)…
- EC
- 2.1.1.-, 2.1.1.361
- UniProt
- P68431, P62805, P04908, P06899, Q9NQR1
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 11 distinct chains · 56% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 97 | 68% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 81 | 63% helix, 9% strand | P62805 |
| C | Histone H2A type 1-B/E | protein | 107 | 57% helix, 6% strand | P04908 |
| D | Histone H2B type 1-J | protein | 93 | 75% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 97 | 65% helix, 4% strand | P68431 |
| G | Histone H2A type 1-B/E | protein | 109 | 53% helix, 6% strand | P04908 |
| H | Histone H2B type 1-J | protein | 92 | 76% helix, 4% strand | P06899 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| K | Isoform 2 of N-lysine methyltransferase KMT5A (EC 2.1.1.-, 2.1.1.361) | protein | 166 | 21% helix, 27% strand | Q9NQR1 |
| F | Histone H4 | protein | 87 | 55% helix, 7% strand | P62805 |
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 | 901 | 0.81 | 0.83 | 78 | empty |
| 2 | 430 | 0.76 | 0.86 | 47 | empty |
| 3 | 1134 | 0.74 | 0.77 | 91 | empty |
| 4 | 326 | 0.72 | 0.85 | 36 | empty |
| 5 | 246 | 0.72 | 0.88 | 34 | empty |
Interfaces
42 interfaces between chains.
- I–J · 6452 Ų buried · 490 hydrogen bonds · nucleic-nucleic
- C–D · 2618 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2573 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 2562 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2504 Ų buried · 20 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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Every structure of UniProt Q9NQR1
- Elsewhere: RCSB PDB 7D1Z · PDBe 7D1Z · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899 · UniProt Q9NQR1
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