Research workbench
Crystal structure of gne-1952 alkylated KRAS G12C in complex with 2H11 clamp
Analyse Crystal structure of gne-1952 alkylated KRAS G12C in complex with 2H11 clamp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RP3
- Type
- protein
- Length
- 592 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2B of GTPase KRAS; Immunoglobulin IgG heavy chain; Immunoglobulin IgG light chain
- EC
- 3.6.5.2
- Ligands
- MKZ, GDP, MG, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 167 | 37% helix, 26% strand | — |
| H | Immunoglobulin IgG heavy chain | protein | 213 | 4% helix, 51% strand | — |
| I | Immunoglobulin IgG light chain | protein | 212 | 7% helix, 50% strand | — |
Ligands and binding sites
- MKZ · 1-[4-[6-chloranyl-7-(5-methyl-1~{H}-indazol-4-yl) quinazolin-4-yl]piperazin-1-yl]propan-1-one · ligand · chains A
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains I
- GOL · Glycerol · additive · 4 copies · chains A, H, I
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.72 | 0.85 | 46 | MKZ, GDP, MG |
| 2 | 703 | 0.67 | 0.75 | 71 | empty |
| 3 | 320 | 0.65 | 0.80 | 38 | GOL, EDO |
| 4 | 74 | 0.44 | 0.81 | 22 | empty |
| 5 | 80 | 0.30 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–I · 1743 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 685 Ų buried · 10 hydrogen bonds · protein-protein
- A–I · 124 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 7RP3 · Crystal structure of GNE-1952 alkylated KRAS 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
- Elsewhere: RCSB PDB 7RP3 · PDBe 7RP3
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