MolNFT v1 · #54317 · protein
WDR5 in complex with an RBBP5 peptide and histone H3 peptide
2XL3 · Wd repeat-containing protein 5: “WDR5 in complex with an RBBP5 peptide and histone H3 peptide”. X-ray diffraction, 3 pockets (best druggability 0.74). MolNFT v1 #54317 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XL3
- Type
- protein
- Length
- 635 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; Retinoblastoma-binding protein 5; Histone H3.1
- UniProt
- P61965, Q8BX09, P68433
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 6 distinct chains · 0% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 5 | protein | 303 | 0% helix, 51% strand | P61965 |
| B | Wd repeat-containing protein 5 | protein | 304 | 0% helix, 51% strand | P61965 |
| C | Retinoblastoma-binding protein 5 | protein | 10 | 0% helix, 0% strand | Q8BX09 |
| D | Histone H3.1 | protein | 5 | 0% helix, 0% strand | P68433 |
| E | Retinoblastoma-binding protein 5 | protein | 9 | 0% helix, 0% strand | Q8BX09 |
| F | Histone H3.1 | protein | 4 | 0% helix, 0% strand | P68433 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 503 | 0.74 | 0.82 | 44 | empty |
| 2 | 497 | 0.72 | 0.81 | 42 | empty |
| 3 | 247 | 0.52 | 0.75 | 44 | empty |
Interfaces
5 interfaces between chains.
- A–C · 502 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 475 Ų buried · 6 hydrogen bonds · protein-protein
- B–E · 440 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 373 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 279 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2XL3 · WDR5 in complex with an RBBP5 peptide and histone H3 peptide · the same entry in another collection · chain F against F, TM-score 1.00
- P61965 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 5 (P61965) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P68433 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68433) · a predicted model of the same protein · chain D against A, TM-score 0.76
- Q8BX09 · AlphaFold monomer V2.0 prediction for retinoblastoma-binding protein 5 (Q8BX09) · a predicted model of the same protein · chain E against A, TM-score 0.60
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 P61965
- Every structure of UniProt Q8BX09
- Every structure of UniProt P68433
- Elsewhere: RCSB PDB 2XL3 · PDBe 2XL3 · UniProt P61965 · UniProt Q8BX09 · UniProt P68433
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