MolNFT v1 · #186769 · protein
Crystal structure of kas G12C in complex with 2H11 clamp
7RP2 · GTPase KRAS: “Crystal structure of kas G12C in complex with 2H11 clamp”. X-ray diffraction, 2 ligands (GDP, MG), 7 pockets (best druggability 0.71). MolNFT v1 #186769 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RP2
- Type
- protein
- Length
- 610 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; Immunoglobulin IgG heavy chain; Immunoglobulin IgG light chain
- UniProt
- P01116
- Ligands
- GDP, MG
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 170 | 36% helix, 26% strand | P01116 |
| H | Immunoglobulin IgG heavy chain | protein | 225 | 7% helix, 48% strand | — |
| I | Immunoglobulin IgG light chain | protein | 215 | 7% helix, 49% strand | — |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CAC · Cacodylate ion · additive · 3 copies · chains H, I, A
- EDO · 1,2-ethanediol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.71 | 0.85 | 44 | GDP, MG |
| 2 | 371 | 0.62 | 0.78 | 45 | CAC |
| 3 | 485 | 0.59 | 0.74 | 59 | CAC |
| 4 | 117 | 0.44 | 0.78 | 32 | empty |
| 5 | 103 | 0.44 | 0.78 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–I · 1950 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 689 Ų buried · 10 hydrogen bonds · protein-protein
- A–I · 105 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 covalent (disulfide, additive adduct).
Compared structures
- 7RP2 · Crystal structure of Kas G12C in complex with 2H11 CLAMP · 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 7RP2 · PDBe 7RP2 · UniProt P01116
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