Research workbench
Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome
Analyse Complex between MLL1-WRAD and an H2B-ubiquitinated nucleosome in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UD5
- Type
- protein + DNA
- Length
- 2,397 residues
- Chains
- 17
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.25
- Source
- Homo sapiens; synthetic construct; Xenopus laevis
- Molecule
- Histone H3; Histone H4; Histone H2A; Histone H2B 1.1; 601 DNA (146-mer); cDNA FLJ56846…
- UniProt
- A0A310TTQ1, P62799, Q6AZJ8, P02281, B4DIJ7, P61964, Q9UBL3, Q15291, J3QS39, Q9C005
- Ligands
- SAH, ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 4.25 · 17 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3 | protein | 97 | 66% helix, 2% strand | A0A310TTQ1 |
| B | Histone H4 | protein | 82 | 60% helix, 5% strand | P62799 |
| C | Histone H2A | protein | 106 | 51% helix, 3% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 96 | 70% helix, 3% strand | P02281 |
| E | Histone H3 | protein | 95 | 69% helix, 3% strand | A0A310TTQ1 |
| F | Histone H4 | protein | 79 | 62% helix, 4% strand | P62799 |
| G | Histone H2A | protein | 105 | 54% helix, 4% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 95 | 73% helix, 2% strand | P02281 |
| I | 601 DNA (146-mer) | dna | 146 | — | — |
| J | 601 DNA (146-mer) | dna | 146 | — | — |
| K | cDNA FLJ56846, highly similar to Zinc finger protein HRX | protein | 175 | 14% helix, 28% strand | B4DIJ7 |
| L | WD repeat-containing protein 5 | protein | 303 | 0% helix, 42% strand | P61964 |
| M | Set1/Ash2 histone methyltransferase complex subunit ASH2 | protein | 328 | 10% helix, 16% strand | Q9UBL3 |
| N | Retinoblastoma-binding protein 5 | protein | 366 | 2% helix, 33% strand | Q15291 |
| O | Polyubiquitin-B | protein | 75 | 25% helix, 20% strand | J3QS39 |
| P | Protein dpy-30 homolog | protein | 52 | 56% helix, 0% strand | Q9C005 |
| Q | Protein dpy-30 homolog | protein | 51 | 57% helix, 0% strand | Q9C005 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 687 | 0.81 | 0.85 | 68 | empty |
| 2 | 759 | 0.78 | 0.82 | 82 | SAH |
| 3 | 328 | 0.78 | 0.88 | 49 | empty |
| 4 | 123 | 0.78 | 0.96 | 28 | empty |
| 5 | 616 | 0.78 | 0.83 | 52 | empty |
Interfaces
55 interfaces between chains.
- I–J · 6743 Ų buried · 620 hydrogen bonds · nucleic-nucleic
- G–H · 2524 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2514 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2504 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2457 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 covalent, 1 disulfide (nonstandard, covalent ligand, disulfide).
Compared structures
- P61964 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 5 (P61964) · a predicted model of the same protein · chain L against A, TM-score 0.96
- P62799 · AlphaFold monomer V2.0 prediction for histone H4 (P62799) · a predicted model of the same protein · chain F against A, TM-score 0.95
- Q15291 · AlphaFold monomer V2.0 prediction for retinoblastoma-binding protein 5 (Q15291) · a predicted model of the same protein · chain N against A, TM-score 0.89
- P02281 · AlphaFold monomer V2.0 prediction for histone H2B 1.1 (P02281) · a predicted model of the same protein · chain H against A, TM-score 0.84
- Q9UBL3 · AlphaFold monomer V2.0 prediction for SET1/ASH2 histone methyltransferase complex subunit… · a predicted model of the same protein · chain M against A, TM-score 0.65
- Q9C005 · AlphaFold monomer V2.0 prediction for protein dpy-30 homolog (Q9C005) · a predicted model of the same protein · chain P against A, TM-score 0.55
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 B4DIJ7
- Every structure of UniProt P61964
- Every structure of UniProt Q9UBL3
- Every structure of UniProt Q15291
- Every structure of UniProt J3QS39
- Every structure of UniProt Q9C005
- Elsewhere: RCSB PDB 7UD5 · PDBe 7UD5 · UniProt A0A310TTQ1 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281 · UniProt B4DIJ7 · UniProt P61964 · UniProt Q9UBL3 · UniProt Q15291 · UniProt J3QS39 · UniProt Q9C005
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