MolNFT v1 · #140687 · protein
Crystal structure of ankb LIR/GABARAP complex
5YIR · Gamma-aminobutyric acid receptor-associated protein: “Crystal structure of ankb LIR/GABARAP complex”. X-ray diffraction, 1 ligand (NI), 4 pockets (best druggability 0.57). MolNFT v1 #140687 on GenesisL1: 3D structure, binding sites…
- PDB
- 5YIR
- Type
- protein
- Length
- 409 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-aminobutyric acid receptor-associated protein; Ankyrin-2
- UniProt
- Q9DCD6, Q01484
- Ligands
- NI
- Pockets
- 4 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B | Gamma-aminobutyric acid receptor-associated protein | protein | 117 | 33% helix, 22% strand | Q9DCD6 |
| C | Ankyrin-2 | protein | 18 | 50% helix, 11% strand | Q01484 |
| G | Ankyrin-2 | protein | 19 | 53% helix, 11% strand | Q01484 |
| H | Ankyrin-2 | protein | 21 | 48% helix, 10% strand | Q01484 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 10 copies · chains D, G, A, B, H
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 | 339 | 0.57 | 0.76 | 31 | NI |
| 2 | 241 | 0.55 | 0.77 | 26 | empty |
| 3 | 85 | 0.32 | 0.74 | 14 | empty |
| 4 | 62 | 0.29 | 0.74 | 15 | NI |
Interfaces
10 interfaces between chains.
- A–G · 933 Ų buried · 14 hydrogen bonds · protein-protein
- B–H · 916 Ų buried · 9 hydrogen bonds · protein-protein
- D–C · 827 Ų buried · 8 hydrogen bonds · protein-protein
- D–G · 196 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 140 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5YIR · Crystal Structure of AnkB LIR/GABARAP complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q9DCD6 · AlphaFold monomer V2.0 prediction for gamma-aminobutyric acid receptor-associated protein… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9DCD6
- Every structure of UniProt Q01484
- Elsewhere: RCSB PDB 5YIR · PDBe 5YIR · UniProt Q9DCD6 · UniProt Q01484
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