MolNFT v1 · #116579 · protein
Crystal structure of ARL13B in complex with ARL3 of chlamydomonas reinhardtii
5DI3 · ADP-ribosylation factor-like protein 13B: “Crystal structure of ARL13B in complex with ARL3 of chlamydomonas reinhardtii”. X-ray diffraction, 2 ligands (GNP, MG), 5 pockets (best druggability 0.57). MolNFT v1 #116579 on GenesisL1…
- PDB
- 5DI3
- Type
- protein
- Length
- 368 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-like protein 13B; ADP-ribosylation factor-like protein 3
- UniProt
- A8INQ0, A8ISN6
- Ligands
- GNP, MG
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | ADP-ribosylation factor-like protein 13B | protein | 204 | 41% helix, 20% strand | A8INQ0 |
| A | ADP-ribosylation factor-like protein 3 | protein | 164 | 34% helix, 26% strand | A8ISN6 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains B, A
- MG · Magnesium ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.57 | 0.83 | 31 | empty |
| 2 | 103 | 0.46 | 0.80 | 23 | GNP, MG |
| 3 | 122 | 0.44 | 0.77 | 26 | GNP, MG |
| 4 | 89 | 0.39 | 0.77 | 17 | empty |
| 5 | 55 | 0.35 | 0.78 | 9 | empty |
Interfaces
1 interface between chains.
- B–A · 1043 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5DI3 · Crystal structure of Arl13B in complex with Arl3 of Chlamydomonas reinhardtii · the same entry in another collection · chain B against B, TM-score 1.00
- A8INQ0 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 13B (A8INQ0) · a predicted model of the same protein · chain B against A, TM-score 0.99
- A8ISN6 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 3 (A8ISN6) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 A8INQ0
- Every structure of UniProt A8ISN6
- Elsewhere: RCSB PDB 5DI3 · PDBe 5DI3 · UniProt A8INQ0 · UniProt A8ISN6
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