Research workbench
Crystal structure of human ADP-ribosylation factor-like 6
Analyse Crystal structure of human ADP-ribosylation factor-like 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H57
- Type
- protein
- Length
- 498 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor-like protein 6
- UniProt
- Q9H0F7
- Ligands
- GTP, MG, UNX
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor-like protein 6 | protein | 165 | 35% helix, 25% strand | Q9H0F7 |
| B | ADP-ribosylation factor-like protein 6 | protein | 167 | 31% helix, 25% strand | Q9H0F7 |
| C | ADP-ribosylation factor-like protein 6 | protein | 166 | 36% helix, 25% strand | Q9H0F7 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- UNX · Unknown atom or ion · ion · 9 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 459 | 0.65 | 0.78 | 53 | UNX |
| 2 | 155 | 0.59 | 0.83 | 27 | MG, GTP |
| 3 | 137 | 0.58 | 0.84 | 25 | MG, GTP |
| 4 | 113 | 0.40 | 0.76 | 22 | MG, GTP |
| 5 | 91 | 0.39 | 0.76 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–C · 722 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 433 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2H57 · Crystal structure of human ADP-ribosylation factor-like 6 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H0F7 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor-like protein 6 (Q9H0F7) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9H0F7
- Elsewhere: RCSB PDB 2H57 · PDBe 2H57 · UniProt Q9H0F7
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