Research workbench
Structure of the rap-rapgap complex
Analyse Structure of the rap-rapgap complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BRW
- Type
- protein
- Length
- 1,172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAP1 GTPase-activating protein 1; RAS-related protein rap-1B
- UniProt
- P47736, P61224
- Ligands
- BEF, GDP, MG
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAP1 GTPase-activating protein 1 | protein | 336 | 26% helix, 24% strand | P47736 |
| B | RAP1 GTPase-activating protein 1 | protein | 337 | 28% helix, 24% strand | P47736 |
| C | RAP1 GTPase-activating protein 1 | protein | 332 | 23% helix, 21% strand | P47736 |
| D | RAS-related protein rap-1B | protein | 167 | 35% helix, 25% strand | P61224 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · chains B, D
- GDP · Guanosine-5'-diphosphate · ligand · chains B, D
- MG · Magnesium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.80 | 0.82 | 113 | MG, BEF, GDP |
| 2 | 103 | 0.77 | 0.97 | 26 | empty |
| 3 | 558 | 0.76 | 0.83 | 71 | empty |
| 4 | 57 | 0.68 | 0.96 | 22 | empty |
| 5 | 308 | 0.55 | 0.75 | 32 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1273 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1217 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 688 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 261 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3BRW · Structure of the Rap-RapGAP complex · 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 D against A, TM-score 0.98
- P47736 · AlphaFold monomer V2.0 prediction for RAP1 GTPase-activating protein 1 (P47736) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P47736
- Every structure of UniProt P61224
- Elsewhere: RCSB PDB 3BRW · PDBe 3BRW · UniProt P47736 · UniProt P61224
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