MolNFT v1 · #183651 · protein
Affimer K69 - KRAS protein complex
7NY8 · GTPase KRAS: “Affimer K69 - KRAS protein complex”. X-ray diffraction, 2 ligands (GDP, MG), 6 pockets (best druggability 0.48). MolNFT v1 #183651 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7NY8
- Type
- protein
- Length
- 523 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; Affimer K69
- UniProt
- P01116
- Ligands
- GDP, MG
- Pockets
- 6 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 168 | 37% helix, 26% strand | P01116 |
| B | GTPase KRAS | protein | 167 | 37% helix, 25% strand | P01116 |
| C | Affimer K69 | protein | 91 | 18% helix, 64% strand | — |
| D | Affimer K69 | protein | 97 | 19% helix, 63% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.48 | 0.79 | 26 | empty |
| 2 | 124 | 0.47 | 0.79 | 27 | GDP, MG |
| 3 | 131 | 0.47 | 0.78 | 29 | GDP, MG |
| 4 | 137 | 0.42 | 0.75 | 19 | empty |
| 5 | 89 | 0.40 | 0.78 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–C · 865 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 721 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 529 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 260 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7NY8 · Affimer K69 - KRAS protein complex · 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 7NY8 · PDBe 7NY8 · UniProt P01116
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