Research workbench
Crystal structure of the arf family small GTPase ARF1 from candida albicans in complex with GDP
Analyse Crystal structure of the arf family small GTPase ARF1 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
- 6PTA
- Type
- protein
- Length
- 658 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor
- UniProt
- P22274
- Ligands
- GDP
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | ADP-ribosylation factor | protein | 165 | 35% helix, 28% strand | P22274 |
| C, D | ADP-ribosylation factor | protein | 164 | 31% helix, 28% strand | P22274 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.76 | 0.78 | 113 | GDP |
| 2 | 450 | 0.62 | 0.76 | 59 | GDP |
| 3 | 82 | 0.45 | 0.81 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–D · 604 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 592 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 292 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 174 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PTA · Crystal structure of the ARF family small GTPase ARF1 from Candida albicans in complex… · the same entry in another collection · chain D against D, TM-score 1.00
- P22274 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor (P22274) · a predicted model of the same protein · chain B against A, TM-score 0.83
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 P22274
- Elsewhere: RCSB PDB 6PTA · PDBe 6PTA · UniProt P22274
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