MolNFT v1 · #128844 · protein
Human KRAS in complex with darpin K27
5O2S · GTPase KRAS: “Human KRAS in complex with darpin K27”. X-ray diffraction, 2 ligands (GDP, MG), 15 pockets (best druggability 0.76). MolNFT v1 #128844 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5O2S
- Type
- protein
- Length
- 1,283 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; Darpin K27
- UniProt
- P01116
- Ligands
- GDP, MG
- Pockets
- 15 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | GTPase KRAS | protein | 165 | 37% helix, 25% strand | P01116 |
| B, D, F, H | Darpin K27 | protein | 156 | 54% helix, 0% strand | — |
| G | GTPase KRAS | protein | 164 | 36% helix, 25% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, C, E, G
- MG · Magnesium ion · metal · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.76 | 0.79 | 86 | empty |
| 2 | 974 | 0.74 | 0.77 | 58 | empty |
| 3 | 561 | 0.70 | 0.79 | 67 | empty |
| 4 | 841 | 0.69 | 0.75 | 64 | GDP, MG |
| 5 | 165 | 0.61 | 0.84 | 29 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1019 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1016 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 947 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 911 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 395 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5O2S · Human KRAS in complex with darpin K27 · 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 5O2S · PDBe 5O2S · UniProt P01116
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