MolNFT v1 · #61800 · protein
Crystal structure of the arfgap domain of human ARFGAP1
3DWD · ADP-ribosylation factor GTPase-activating protein 1: “Crystal structure of the arfgap domain of human ARFGAP1”. X-ray diffraction, 2 ligands (ZN, UNX), 2 pockets (best druggability 0.35). MolNFT v1 #61800 on GenesisL1: 3D structure…
- PDB
- 3DWD
- Type
- protein
- Length
- 230 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor GTPase-activating protein 1
- UniProt
- Q8N6T3
- Ligands
- ZN, UNX
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosylation factor GTPase-activating protein 1 | protein | 116 | 50% helix, 9% strand | Q8N6T3 |
| B | ADP-ribosylation factor GTPase-activating protein 1 | protein | 114 | 51% helix, 10% strand | Q8N6T3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- UNX · Unknown atom or ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.35 | 0.74 | 20 | empty |
| 2 | 54 | 0.31 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 68 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3DWD · Crystal structure of the ArfGAP domain of human ARFGAP1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8N6T3 · AlphaFold monomer V2.0 prediction for ADP-ribosylation factor GTPase- activating protein… · a predicted model of the same protein · chain A 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 Q8N6T3
- Elsewhere: RCSB PDB 3DWD · PDBe 3DWD · UniProt Q8N6T3
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