MolNFT v1 · #133448 · protein
EPB41L3 pandda analysis group deposition -- crystal structure of the ferm domain of human EPB41L3 in complex with Z2856434868
5RYZ · 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 (NVY), 4 pockets (best druggability 0.68). MolNFT v1…
- PDB
- 5RYZ
- 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
- NVY
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2 of band 4.1-like protein 3 | protein | 284 | 37% helix, 25% strand | Q9Y2J2 |
Ligands and binding sites
- NVY · 1-ethyl-N-(2-fluorophenyl)piperidin-4-amine · ligand · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.68 | 0.80 | 46 | DMS, EDO |
| 2 | 135 | 0.51 | 0.80 | 20 | empty |
| 3 | 90 | 0.41 | 0.78 | 18 | empty |
| 4 | 80 | 0.38 | 0.77 | 23 | NVY |
Compared structures
- 5RYZ · 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 5RYZ · PDBe 5RYZ · UniProt Q9Y2J2
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