MolNFT v1 · #186765 · protein
KRAS G12D mutant in complex with gmppcp and cyclic peptide mp-9903
7ROV · Isoform 2B of GTPase KRAS: “KRAS G12D mutant in complex with gmppcp and cyclic peptide mp-9903”. X-ray diffraction, 3 ligands (060, GCP, MG), 3 pockets (best druggability 0.48). MolNFT v1 #186765 on GenesisL1: 3D structure, binding…
- PDB
- 7ROV
- Type
- protein
- Length
- 360 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2B of GTPase KRAS; Cyclic peptide mp-9903
- EC
- 3.6.5.2
- UniProt
- P01116
- Ligands
- 060, GCP, MG
- Pockets
- 3 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 168 | 36% helix, 26% strand | P01116 |
| E, F | Cyclic peptide mp-9903 | protein | 12 | 0% helix, 0% strand | — |
Ligands and binding sites
- 060 · S-methyl-D-cysteine · ligand · 2 copies · chains A, E, B, F
- GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.48 | 0.78 | 27 | GCP, MG |
| 2 | 154 | 0.48 | 0.77 | 23 | empty |
| 3 | 105 | 0.36 | 0.74 | 25 | GCP, MG |
Interfaces
3 interfaces between chains.
- A–E · 611 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 589 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 396 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 7ROV · KRAS G12D Mutant in complex with GMPPCP and cyclic peptide MP-9903 · 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 7ROV · PDBe 7ROV · UniProt P01116
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