MolNFT v1 · #133442 · protein
EPB41L3 pandda analysis group deposition -- crystal structure of the ferm domain of human EPB41L3 in complex with Z54226006
5RYT · Isoform 2 of band 4.1-like protein 3: “EPB41L3 pandda analysis group deposition -- crystal structure of the ferm domain of human EPB41L3 in complex…”. X-ray diffraction, 1 ligand (NX7), 4 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 5RYT
- Type
- protein
- Length
- 284 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2 of band 4.1-like protein 3
- UniProt
- Q9Y2J2
- Ligands
- NX7
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of band 4.1-like protein 3 | protein | 284 | 35% helix, 25% strand | Q9Y2J2 |
Ligands and binding sites
- NX7 · (2,6-difluorophenyl)(pyrrolidin-1-yl)methanone · ligand · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 482 | 0.72 | 0.81 | 46 | EDO |
| 2 | 94 | 0.41 | 0.77 | 19 | NX7 |
| 3 | 93 | 0.36 | 0.75 | 23 | DMS, EDO |
| 4 | 51 | 0.28 | 0.75 | 16 | DMS |
Compared structures
- 5RYT · EPB41L3 PanDDA analysis group deposition -- Crystal Structure of the FERM domain of human… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y2J2 · AlphaFold monomer V2.0 prediction for band 4.1-like protein 3 (Q9Y2J2) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9Y2J2
- Elsewhere: RCSB PDB 5RYT · PDBe 5RYT · UniProt Q9Y2J2
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