MolNFT v1 · #111367 · protein
P107 pocket domain complexed with LIN52 peptide
4YOS · Retinoblastoma-like protein 1,RETINOBLASTOMA-like protein 1: “P107 pocket domain complexed with LIN52 peptide”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.42). MolNFT v1 #111367 on GenesisL1: 3D structure…
- PDB
- 4YOS
- Type
- protein
- Length
- 353 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoblastoma-like protein 1,RETINOBLASTOMA-like protein 1; Protein lin-52 homolog
- UniProt
- P28749, L5LUA8, Q5ZJQ3
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoblastoma-like protein 1,RETINOBLASTOMA-like protein 1 | protein | 340 | 65% helix, 1% strand | P28749, L5LUA8 |
| E | Protein lin-52 homolog | protein | 13 | 0% helix, 0% strand | Q5ZJQ3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.42 | 0.74 | 24 | empty |
| 2 | 125 | 0.38 | 0.74 | 29 | EDO |
Interfaces
1 interface between chains.
- A–E · 613 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4YOS · p107 pocket domain complexed with LIN52 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P28749 · AlphaFold monomer V2.0 prediction for retinoblastoma-like protein 1 (P28749) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q5ZJQ3 · AlphaFold monomer V2.0 prediction for protein lin-52 homolog (Q5ZJQ3) · a predicted model of the same protein · chain E against A, TM-score 0.24
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 P28749
- Every structure of UniProt L5LUA8
- Every structure of UniProt Q5ZJQ3
- Elsewhere: RCSB PDB 4YOS · PDBe 4YOS · UniProt P28749 · UniProt L5LUA8 · UniProt Q5ZJQ3
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