MolNFT v1 · #160747 · protein
Crystal structure of the arf family small GTPase ARF1 from candida albicans in complex with GDP
6PTA · ADP-ribosylation factor: “Crystal structure of the arf family small GTPase ARF1 from candida albicans in complex with GDP”. X-ray diffraction, 1 ligand (GDP), 3 pockets (best druggability 0.76). MolNFT v1 #160747 on GenesisL1: 3D…
- 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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