Research workbench
Crystal structure of the ARF1:ARHGAP21-arfbd complex
Analyse Crystal structure of the ARF1:ARHGAP21-arfbd complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J59
- Type
- protein
- Length
- 1,669 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosylation factor 1; Rho-GTPase activating protein 10
- UniProt
- P84078, Q8NI19
- Ligands
- GTP, MG, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | ADP-ribosylation factor 1 | protein | 165 | 36% helix, 27% strand | P84078 |
| M, R | Rho-GTPase activating protein 10 | protein | 113 | 31% helix, 34% strand | Q8NI19 |
| N, P, Q | Rho-GTPase activating protein 10 | protein | 114 | 30% helix, 33% strand | Q8NI19 |
| O | Rho-GTPase activating protein 10 | protein | 111 | 29% helix, 34% strand | Q8NI19 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains M, N, O, P, Q, R
- DIO · 1,4-diethylene dioxide · additive · 3 copies · chains A, D, B, E, C, F
- EDO · 1,2-ethanediol · additive · 3 copies · chains C, E, B, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1141 | 0.82 | 0.83 | 96 | empty |
| 2 | 334 | 0.74 | 0.85 | 41 | empty |
| 3 | 536 | 0.72 | 0.81 | 65 | DIO, EDO |
| 4 | 837 | 0.72 | 0.77 | 83 | DIO |
| 5 | 184 | 0.60 | 0.82 | 34 | DIO |
Interfaces
19 interfaces between chains.
- D–P · 853 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 853 Ų buried · 17 hydrogen bonds · protein-protein
- A–M · 852 Ų buried · 3 hydrogen bonds · protein-protein
- B–N · 852 Ų buried · 3 hydrogen bonds · protein-protein
- F–R · 848 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2J59 · Crystal structure of the ARF1:ARHGAP21-ArfBD complex · the same entry in another collection · chain R against R, 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 P84078
- Every structure of UniProt Q8NI19
- Elsewhere: RCSB PDB 2J59 · PDBe 2J59 · UniProt P84078 · UniProt Q8NI19
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