Research workbench
Structure of human ADP-ribosylation factor-like 5 (ARL5)
Analyse Structure of human ADP-ribosylation factor-like 5 (ARL5) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H16
- Type
- protein
- Length
- 603 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-like protein 5A
- UniProt
- Q9Y689
- Ligands
- GDP, UNX
- Pockets
- 9 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor-like protein 5A | protein | 149 | 30% helix, 28% strand | Q9Y689 |
| B | ADP-ribosylation factor-like protein 5A | protein | 149 | 30% helix, 29% strand | Q9Y689 |
| C | ADP-ribosylation factor-like protein 5A | protein | 152 | 28% helix, 27% strand | Q9Y689 |
| D | ADP-ribosylation factor-like protein 5A | protein | 153 | 29% helix, 27% strand | Q9Y689 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, D, B, C
- UNX · Unknown atom or ion · ion · 28 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.51 | 0.78 | 26 | UNX |
| 2 | 136 | 0.51 | 0.80 | 21 | UNX |
| 3 | 119 | 0.44 | 0.78 | 22 | UNX |
| 4 | 56 | 0.42 | 0.82 | 12 | empty |
| 5 | 75 | 0.42 | 0.80 | 22 | UNX |
Interfaces
4 interfaces between chains.
- A–C · 651 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 626 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 622 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 602 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 2H16 · Structure of human ADP-ribosylation factor-like 5 (ARL5) · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y689 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 5A (Q9Y689) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9Y689
- Elsewhere: RCSB PDB 2H16 · PDBe 2H16 · UniProt Q9Y689
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