MolNFT v1 · #54316 · protein
WDR5 in complex with an RBBP5 peptide recruited to novel site
2XL2 · Wd repeat-containing protein 5: “WDR5 in complex with an RBBP5 peptide recruited to novel site”. X-ray diffraction, 5 pockets (best druggability 0.76). MolNFT v1 #54316 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XL2
- Type
- protein
- Length
- 628 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 5; Retinoblastoma-binding protein 5
- UniProt
- P61965, Q8BX09
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Wd repeat-containing protein 5 | protein | 304 | 0% helix, 52% strand | P61965 |
| C, D | Retinoblastoma-binding protein 5 | protein | 10 | 0% helix, 0% strand | Q8BX09 |
Ligands and binding sites
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.76 | 0.81 | 69 | empty |
| 2 | 469 | 0.72 | 0.81 | 33 | empty |
| 3 | 269 | 0.64 | 0.81 | 36 | empty |
| 4 | 164 | 0.47 | 0.76 | 28 | empty |
| 5 | 77 | 0.33 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 497 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 495 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 255 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2XL2 · WDR5 in complex with an RBBP5 peptide recruited to novel site · the same entry in another collection · chain A against A, 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
- Q8BX09 · AlphaFold monomer V2.0 prediction for retinoblastoma-binding protein 5 (Q8BX09) · a predicted model of the same protein · chain C against A, TM-score 0.61
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
- Elsewhere: RCSB PDB 2XL2 · PDBe 2XL2 · UniProt P61965 · UniProt Q8BX09
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