MolNFT v1 · #124522 · protein
RASIP1 ra domain in complex with RAP1B
5KHO · RAS-interacting protein 1: “RASIP1 ra domain in complex with RAP1B”. X-ray diffraction, 2 ligands (GNP, MG), 6 pockets (best druggability 0.61). MolNFT v1 #124522 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KHO
- Type
- protein
- Length
- 541 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-interacting protein 1; RAS-related protein rap-1B
- UniProt
- Q5U651, P61224
- Ligands
- GNP, MG
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-interacting protein 1 | protein | 103 | 26% helix, 37% strand | Q5U651 |
| B | RAS-interacting protein 1 | protein | 106 | 30% helix, 33% strand | Q5U651 |
| C | RAS-related protein rap-1B | protein | 165 | 37% helix, 27% strand | P61224 |
| D | RAS-related protein rap-1B | protein | 167 | 35% helix, 26% strand | P61224 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains C, D
- MG · Magnesium ion · metal · 2 copies · chains C, D
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.61 | 0.79 | 41 | MG, GNP |
| 2 | 250 | 0.57 | 0.78 | 38 | MG, GNP |
| 3 | 126 | 0.46 | 0.78 | 26 | empty |
| 4 | 60 | 0.36 | 0.78 | 18 | empty |
| 5 | 68 | 0.33 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 867 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 571 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 549 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5KHO · Rasip1 RA domain in complex with Rap1B · the same entry in another collection · chain D against D, TM-score 1.00
- P61224 · AlphaFold monomer V2.0 prediction for RAS-related protein rap-1B (P61224) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q5U651 · AlphaFold monomer V2.0 prediction for RAS-interacting protein 1 (Q5U651) · 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 Q5U651
- Every structure of UniProt P61224
- Elsewhere: RCSB PDB 5KHO · PDBe 5KHO · UniProt Q5U651 · UniProt P61224
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