MolNFT v1 · #138974 · protein + DNA
Complex of SNF2-nucleosome complex with SNF2 bound to SHL2 of the nucleosome
5X0Y · Histone H3.2: “Complex of SNF2-nucleosome complex with SNF2 bound to SHL2 of the nucleosome”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #138974 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5X0Y
- Type
- protein + DNA
- Length
- 1,641 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1; DNA (167-mer); Transcription…
- EC
- 3.6.4.-
- UniProt
- P84233, P62799, Q6AZJ8, P02281, P22082
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 58% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.2 | protein | 98 | 63% helix, 3% strand | P84233 |
| B | Histone H4 | protein | 87 | 55% helix, 5% strand | P62799 |
| C, G | Histone H2A | protein | 107 | 59% helix, 6% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 93 | 71% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 95 | 65% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 86 | 62% helix, 7% strand | P62799 |
| I | DNA (167-mer) | dna | 146 | — | — |
| J | DNA (167-mer) | dna | 146 | — | — |
| O | Transcription regulatory protein SNF2 (EC 3.6.4.-) | protein | 583 | 54% helix, 8% strand | P22082 |
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 | 729 | 0.87 | 0.90 | 77 | empty |
| 2 | 186 | 0.80 | 0.94 | 40 | empty |
| 3 | 104 | 0.76 | 0.96 | 21 | empty |
| 4 | 626 | 0.76 | 0.82 | 62 | empty |
| 5 | 319 | 0.73 | 0.86 | 39 | empty |
Interfaces
40 interfaces between chains.
- I–J · 6573 Ų buried · 788 hydrogen bonds · nucleic-nucleic
- E–F · 2454 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 2410 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2375 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2292 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5X0Y · Complex of Snf2-Nucleosome complex with Snf2 bound to SHL2 of the nucleosome · the same entry in another collection · chain O against O, TM-score 1.00
- P22082 · AlphaFold monomer V2.0 prediction for transcription regulatory protein SNF2 (P22082) · a predicted model of the same protein · chain O against A, TM-score 0.93
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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt P22082
- Elsewhere: RCSB PDB 5X0Y · PDBe 5X0Y · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt P22082
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