Research workbench
K-RASG12D(GNP)/R11.1.6 complex
Analyse K-RASG12D(GNP)/R11.1.6 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UFQ
- Type
- protein
- Length
- 446 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; R11.1.6
- UniProt
- P01116
- Ligands
- GNP, MG, CA, CD, CL
- Pockets
- 5 · best druggability 0.42
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GTPase KRAS | protein | 166 | 37% helix, 25% strand | P01116 |
| C | R11.1.6 | protein | 56 | 18% helix, 48% strand | — |
| D | R11.1.6 | protein | 58 | 12% helix, 55% strand | — |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CD · Cadmium ion · metal · 2 copies · chains A, B, D
- CL · Chloride ion · ion · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.42 | 0.77 | 21 | empty |
| 2 | 102 | 0.41 | 0.77 | 25 | GNP, MG |
| 3 | 94 | 0.40 | 0.77 | 24 | GNP, MG |
| 4 | 79 | 0.40 | 0.78 | 17 | empty |
| 5 | 54 | 0.36 | 0.79 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 838 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 250 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 172 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5UFQ · K-RasG12D(GNP)/R11.1.6 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 5UFQ · PDBe 5UFQ · UniProt P01116
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