MolNFT v1 · #184265 · protein
Crystal structure of the UNC119B ARL3 complex
7OK7 · ADP-ribosylation factor-like protein 3: “Crystal structure of the UNC119B ARL3 complex”. X-ray diffraction, 3 ligands (GNP, MG, PO4), 20 pockets (best druggability 0.78). MolNFT v1 #184265 on GenesisL1: 3D structure, binding sites…
- PDB
- 7OK7
- Type
- protein
- Length
- 2,084 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-like protein 3; Protein unc-119 homolog B
- UniProt
- Q9WUL7, A6NIH7
- Ligands
- GNP, MG, PO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 12 distinct chains · 23% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor-like protein 3 | protein | 174 | 32% helix, 24% strand | Q9WUL7 |
| B | ADP-ribosylation factor-like protein 3 | protein | 177 | 32% helix, 23% strand | Q9WUL7 |
| C | ADP-ribosylation factor-like protein 3 | protein | 183 | 33% helix, 23% strand | Q9WUL7 |
| D | ADP-ribosylation factor-like protein 3 | protein | 177 | 30% helix, 24% strand | Q9WUL7 |
| E | ADP-ribosylation factor-like protein 3 | protein | 174 | 34% helix, 24% strand | Q9WUL7 |
| F | ADP-ribosylation factor-like protein 3 | protein | 180 | 34% helix, 23% strand | Q9WUL7 |
| G | Protein unc-119 homolog B | protein | 175 | 12% helix, 48% strand | A6NIH7 |
| H | Protein unc-119 homolog B | protein | 172 | 12% helix, 48% strand | A6NIH7 |
| I | Protein unc-119 homolog B | protein | 171 | 12% helix, 48% strand | A6NIH7 |
| J | Protein unc-119 homolog B | protein | 174 | 11% helix, 47% strand | A6NIH7 |
| K | Protein unc-119 homolog B | protein | 165 | 13% helix, 48% strand | A6NIH7 |
| L | Protein unc-119 homolog B | protein | 162 | 13% helix, 51% strand | A6NIH7 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · 6 copies · chains C, H, B, G, A, I, J, E, K, L
- GOL · Glycerol · additive · 4 copies · chains G, H, I, J
- EDO · 1,2-ethanediol · additive · 2 copies · chains G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.78 | 0.85 | 59 | GOL, EDO |
| 2 | 518 | 0.78 | 0.84 | 62 | GOL |
| 3 | 451 | 0.77 | 0.85 | 58 | empty |
| 4 | 545 | 0.76 | 0.83 | 62 | GOL, EDO |
| 5 | 487 | 0.76 | 0.84 | 59 | GOL |
Interfaces
18 interfaces between chains.
- C–F · 1198 Ų buried · 7 hydrogen bonds · protein-protein
- A–I · 1061 Ų buried · 20 hydrogen bonds · protein-protein
- E–K · 1026 Ų buried · 20 hydrogen bonds · protein-protein
- C–H · 1008 Ų buried · 21 hydrogen bonds · protein-protein
- B–G · 978 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7OK7 · Crystal structure of the UNC119B ARL3 complex · the same entry in another collection · chain L against L, TM-score 1.00
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 Q9WUL7
- Every structure of UniProt A6NIH7
- Elsewhere: RCSB PDB 7OK7 · PDBe 7OK7 · UniProt Q9WUL7 · UniProt A6NIH7
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