Research workbench
Crystal structure of RAP.GMPPNP in complex with the RAS- binding-domain of C-RAF1 kinase (rafrbd).
Analyse Crystal structure of RAP.GMPPNP in complex with the RAS- binding-domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1C1Y
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein rap-1A; Proto-onkogene SERINE/THREONINE protein kinase RAF-1
- EC
- 2.7.1.-
- UniProt
- P62834, P04049
- Ligands
- GTP, MG, CA
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RAS-related protein rap-1A | protein | 167 | 36% helix, 26% strand | P62834 |
| B | Proto-onkogene SERINE/THREONINE protein kinase RAF-1 (EC 2.7.1.-) | protein | 77 | 26% helix, 42% strand | P04049 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CA · Calcium ion · metal · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.71 | 0.84 | 47 | MG, GTP |
| 2 | 159 | 0.46 | 0.76 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 714 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1C1Y · Crystal structure of RAP.GMPPNP in complex with the RAS-binding-domain of C-RAF1 kinase… · the same entry in another collection · chain A against A, TM-score 1.00
- P62834 · AlphaFold monomer V2.0 prediction for RAS-related protein rap-1A (P62834) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P04049 · AlphaFold monomer V2.0 prediction for RAF proto-oncogene SERINE/THREONINE-protein kinase… · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P62834
- Every structure of UniProt P04049
- Elsewhere: RCSB PDB 1C1Y · PDBe 1C1Y · UniProt P62834 · UniProt P04049
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