Research workbench
Crystal structure analysis of RAC1-gmppnp in complex with arfaptin
Analyse Crystal structure analysis of RAC1-gmppnp in complex with arfaptin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1I4T
- Type
- protein
- Length
- 536 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arfaptin 2; RAS-related C3 botulinum toxin substrate 1
- UniProt
- P53365, P63000
- Ligands
- GNP, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arfaptin 2 | protein | 180 | 90% helix, 0% strand | P53365 |
| B | Arfaptin 2 | protein | 179 | 83% helix, 0% strand | P53365 |
| D | RAS-related C3 botulinum toxin substrate 1 | protein | 177 | 33% helix, 22% strand | P63000 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains D
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 99 | 0.79 | 0.98 | 24 | empty |
| 2 | 218 | 0.56 | 0.79 | 28 | empty |
| 3 | 96 | 0.53 | 0.83 | 18 | empty |
| 4 | 271 | 0.52 | 0.75 | 31 | MG, GNP |
| 5 | 89 | 0.50 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2153 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 766 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 188 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1I4T · Crystal structure analysis of RAC1-gmppnp in complex with arfaptin · the same entry in another collection · chain A against A, TM-score 1.00
- P63000 · AlphaFold monomer V2.0 prediction for RAS-related C3 botulinum toxin substrate 1 (P63000) · a predicted model of the same protein · chain D against A, TM-score 0.96
- P53365 · AlphaFold monomer V2.0 prediction for arfaptin-2 (P53365) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P53365
- Every structure of UniProt P63000
- Elsewhere: RCSB PDB 1I4T · PDBe 1I4T · UniProt P53365 · UniProt P63000
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