Research workbench
Crystal structure of M-RAS P40D/D41E/L51R in complex with gppnhp
Analyse Crystal structure of M-RAS P40D/D41E/L51R in complex with gppnhp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KKO
- Type
- protein
- Length
- 506 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RAS-related protein M-RAS
- UniProt
- O08989
- Ligands
- GNP, MG, SO4
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RAS-related protein M-RAS | protein | 169 | 36% helix, 27% strand | O08989 |
| P | RAS-related protein M-RAS | protein | 168 | 39% helix, 27% strand | O08989 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, B, P
- MG · Magnesium ion · metal · 3 copies · chains A, B, P
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, P
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 | 293 | 0.60 | 0.79 | 40 | GNP, MG |
| 2 | 163 | 0.59 | 0.83 | 30 | GNP, MG |
| 3 | 143 | 0.54 | 0.81 | 28 | GNP, MG |
| 4 | 364 | 0.52 | 0.72 | 40 | SO4 |
| 5 | 120 | 0.41 | 0.75 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–B · 621 Ų buried · 6 hydrogen bonds · protein-protein
- A–P · 149 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3KKO · Crystal structure of M-Ras P40D/D41E/L51R in complex with GppNHp · the same entry in another collection · chain B against B, TM-score 1.00
- O08989 · AlphaFold monomer V2.0 prediction for RAS-related protein M-RAS (O08989) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O08989
- Elsewhere: RCSB PDB 3KKO · PDBe 3KKO · UniProt O08989
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