MolNFT v1 · #163338 · protein + DNA
Structure of ledgf pwwp domain bound H3K36 methylated nucleosome
6S01 · Histone H3: “Structure of ledgf pwwp domain bound H3K36 methylated nucleosome”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #163338 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6S01
- Type
- protein + DNA
- Length
- 1,153 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B 1.1; Wisdom 601 DNA (165-mer); PC4 and…
- UniProt
- A0A310TTQ1, P62799, Q6AZJ8, P02281, O75475
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 9 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 100 | 59% helix, 4% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 82 | 59% helix, 9% strand | P62799 |
| C, G | Histone H2A | protein | 107 | 50% helix, 7% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 94 | 73% helix, 4% strand | P02281 |
| E | Histone H3 | protein | 97 | 63% helix, 4% strand | A0A310TTQ1 |
| F | Histone H4 | protein | 86 | 57% helix, 8% strand | P62799 |
| I | Wisdom 601 DNA (165-mer) | dna | 150 | — | — |
| J | Wisdom 601 DNA (165-mer) | dna | 150 | — | — |
| K | PC4 and SFRS1-interacting protein | protein | 86 | 8% helix, 21% strand | O75475 |
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 | 849 | 0.81 | 0.84 | 99 | empty |
| 2 | 393 | 0.75 | 0.86 | 52 | empty |
| 3 | 452 | 0.74 | 0.83 | 46 | empty |
| 4 | 741 | 0.73 | 0.79 | 62 | empty |
| 5 | 321 | 0.67 | 0.83 | 39 | empty |
Interfaces
39 interfaces between chains.
- I–J · 6925 Ų buried · 775 hydrogen bonds · nucleic-nucleic
- E–F · 2808 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2610 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2583 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2570 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6S01 · Structure of LEDGF PWWP domain bound H3K36 methylated nucleosome · the same entry in another collection · chain K against K, TM-score 1.00
- O75475 · AlphaFold monomer V2.0 prediction for PC4 and SFRS1-interacting protein (O75475) · a predicted model of the same protein · chain K against A, TM-score 0.82
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 Q6AZJ8
- Every structure of UniProt P02281
- Every structure of UniProt O75475
- Elsewhere: RCSB PDB 6S01 · PDBe 6S01 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt O75475
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