MolNFT v1 · #150266 · protein
KRAS-169 Q61H gppnhp
6GOG · GTPase KRAS: “KRAS-169 Q61H gppnhp”. X-ray diffraction, 2 ligands (GNP, MG), 13 pockets (best druggability 0.78). MolNFT v1 #150266 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6GOG
- Type
- protein
- Length
- 1,026 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GNP, MG
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 170 | 36% helix, 26% strand | P01116 |
| B | GTPase KRAS | protein | 173 | 38% helix, 26% strand | P01116 |
| C, F | GTPase KRAS | protein | 172 | 38% helix, 26% strand | P01116 |
| D | GTPase KRAS | protein | 168 | 37% helix, 26% strand | P01116 |
| E | GTPase KRAS | protein | 171 | 37% helix, 26% strand | P01116 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- CIT · Citric acid · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 540 | 0.78 | 0.85 | 74 | empty |
| 2 | 1116 | 0.78 | 0.80 | 106 | empty |
| 3 | 505 | 0.68 | 0.79 | 55 | GNP, MG |
| 4 | 399 | 0.64 | 0.78 | 52 | GNP, MG |
| 5 | 206 | 0.63 | 0.83 | 34 | GNP, MG |
Interfaces
12 interfaces between chains.
- B–E · 761 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 673 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 663 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 362 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 349 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6GOG · KRAS-169 Q61H gppnhp · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6GOG · PDBe 6GOG · UniProt P01116
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