Research workbench
Crystal structure of the arf family small GTPase ARF2 from candida albicans in complex with GDP
Analyse Crystal structure of the arf family small GTPase ARF2 from candida albicans in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UF8
- Type
- protein
- Length
- 641 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Potential ADP-ribosylation factor
- UniProt
- Q5AND9
- Ligands
- GDP
- Pockets
- 7 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Potential ADP-ribosylation factor | protein | 161 | 34% helix, 33% strand | Q5AND9 |
| B | Potential ADP-ribosylation factor | protein | 159 | 33% helix, 32% strand | Q5AND9 |
| D | Potential ADP-ribosylation factor | protein | 160 | 33% helix, 29% strand | Q5AND9 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 204 | 0.53 | 0.77 | 27 | empty |
| 2 | 90 | 0.40 | 0.76 | 11 | empty |
| 3 | 97 | 0.38 | 0.75 | 17 | empty |
| 4 | 137 | 0.38 | 0.73 | 27 | empty |
| 5 | 81 | 0.38 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 380 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 200 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5UF8 · Crystal structure of the ARF family small GTPase ARF2 from Candida albicans in complex… · the same entry in another collection · chain A against A, 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 Q5AND9
- Elsewhere: RCSB PDB 5UF8 · PDBe 5UF8 · UniProt Q5AND9
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