MolNFT v1 · #181675 · protein + DNA
Cryo-EM structure of nucleosome containing mouse histone variant H2A.Z
7M1X · DNA (136-mer): “Cryo-EM structure of nucleosome containing mouse histone variant H2A.Z”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #181675 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7M1X
- Type
- protein + DNA
- Length
- 1,018 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (136-mer); Histone H3; Histone H4; Histone H2A.Z; Histone H2B 1.1
- UniProt
- A0A310TTQ1, P62799, P0C0S6, P02281
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 9 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA (136-mer) | dna | 136 | — | — |
| J | DNA (136-mer) | dna | 136 | — | — |
| A | Histone H3 | protein | 95 | 68% helix, 3% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 80 | 64% helix, 5% strand | P62799 |
| C | Histone H2A.Z | protein | 103 | 54% helix, 5% strand | P0C0S6 |
| D, H | Histone H2B 1.1 | protein | 95 | 73% helix, 4% strand | P02281 |
| E | Histone H3 | protein | 97 | 68% helix, 4% strand | A0A310TTQ1 |
| F | Histone H4 | protein | 86 | 59% helix, 6% strand | P62799 |
| G | Histone H2A.Z | protein | 95 | 62% helix, 5% strand | P0C0S6 |
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 | 1079 | 0.81 | 0.83 | 105 | empty |
| 2 | 419 | 0.73 | 0.84 | 40 | empty |
| 3 | 753 | 0.70 | 0.77 | 52 | empty |
| 4 | 768 | 0.70 | 0.77 | 43 | empty |
| 5 | 771 | 0.69 | 0.77 | 56 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6098 Ų buried · 427 hydrogen bonds · nucleic-nucleic
- G–H · 2682 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2666 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 2656 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2528 Ų buried · 16 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 A0A310TTQ1
- Every structure of UniProt P62799
- Every structure of UniProt P0C0S6
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 7M1X · PDBe 7M1X · UniProt A0A310TTQ1 · UniProt P62799 · UniProt P0C0S6 · UniProt P02281
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