MolNFT v1 · #139334 · protein
Crystal structure of human K-RAS G12D mutant in complex with GDP and cyclic inhibitory peptide
5XCO · GTPase KRAS: “Crystal structure of human K-RAS G12D mutant in complex with GDP and cyclic inhibitory peptide”. X-ray diffraction, 3 ligands (ACE, GDP, NH2), 2 pockets (best druggability 0.45). MolNFT v1 #139334 on GenesisL1: 3D…
- PDB
- 5XCO
- Type
- protein
- Length
- 189 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; ACE-arg-arg-arg-arg-cys-pro-leu-tyr-ile-ser-tyr-asp-pro…
- UniProt
- P01116
- Ligands
- ACE, GDP, NH2
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 170 | 37% helix, 25% strand | P01116 |
| B | ACE-arg-arg-arg-arg-cys-pro-leu-tyr-ile-ser-tyr-asp-pro- val-cys-arg-arg-arg-arg-NH2 | protein | 19 | 21% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- NH2 · Amino group · ion · chains B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 163 | 0.45 | 0.75 | 29 | GDP |
| 2 | 123 | 0.42 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 719 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5XCO · Crystal structure of human K-Ras G12D Mutant in complex with GDP and Cyclic Inhibitory… · 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 5XCO · PDBe 5XCO · UniProt P01116
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