MolNFT v1 · #158996 · protein
Crystal structure of wild-type KRAS (gmppnp-bound) in complex with gap-related domain (grd) of neurofibromin (NF1)
6OB2 · GTPase KRAS: “Crystal structure of wild-type KRAS (gmppnp-bound) in complex with gap-related domain (grd) of neurofibromin…”. X-ray diffraction, 3 ligands (GNP, MG, CL), 13 pockets (best druggability 0.77). MolNFT v1 #158996 on…
- PDB
- 6OB2
- Type
- protein
- Length
- 820 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; Neurofibromin
- UniProt
- P01116, P21359
- Ligands
- GNP, MG, CL
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 169 | 40% helix, 26% strand | P01116 |
| B | Neurofibromin | protein | 241 | 73% helix, 0% strand | P21359 |
| C | GTPase KRAS | protein | 165 | 38% helix, 27% strand | P01116 |
| D | Neurofibromin | protein | 245 | 71% helix, 0% strand | P21359 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
- IMD · Imidazole · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.77 | 0.87 | 58 | GNP, MG |
| 2 | 833 | 0.75 | 0.79 | 88 | GNP, MG |
| 3 | 361 | 0.67 | 0.81 | 47 | empty |
| 4 | 223 | 0.63 | 0.82 | 35 | empty |
| 5 | 187 | 0.60 | 0.82 | 32 | GOL |
Interfaces
4 interfaces between chains.
- A–B · 1235 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1087 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 340 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 242 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6OB2 · Crystal structure of wild-type KRAS (GMPPNP-bound) in complex with GAP-related domain… · the same entry in another collection · chain C against C, TM-score 1.00
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 P01116
- Every structure of UniProt P21359
- Elsewhere: RCSB PDB 6OB2 · PDBe 6OB2 · UniProt P01116 · UniProt P21359
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