MolNFT v1 · #136422 · protein
Crystal structure of human KRAS G12D mutant in complex with gdpnp
5USJ · GTPase KRAS: “Crystal structure of human KRAS G12D mutant in complex with gdpnp”. X-ray diffraction, 2 ligands (GNP, MG), 11 pockets (best druggability 0.86). MolNFT v1 #136422 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5USJ
- Type
- protein
- Length
- 1,010 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GNP, MG
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 168 | 38% helix, 26% strand | P01116 |
| B | GTPase KRAS | protein | 170 | 39% helix, 26% strand | P01116 |
| C | GTPase KRAS | protein | 171 | 39% helix, 26% strand | P01116 |
| D | GTPase KRAS | protein | 162 | 36% helix, 27% strand | P01116 |
| E | GTPase KRAS | protein | 169 | 39% helix, 26% strand | P01116 |
| F | GTPase KRAS | protein | 170 | 36% helix, 26% strand | P01116 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.86 | 0.87 | 96 | empty |
| 2 | 586 | 0.82 | 0.87 | 68 | empty |
| 3 | 434 | 0.76 | 0.85 | 55 | empty |
| 4 | 140 | 0.68 | 0.89 | 21 | empty |
| 5 | 188 | 0.58 | 0.81 | 36 | MG, GNP |
Interfaces
11 interfaces between chains.
- A–B · 615 Ų buried · 9 hydrogen bonds · protein-protein
- B–F · 584 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 571 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 543 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 488 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5USJ · Crystal Structure of human KRAS G12D mutant in complex with GDPNP · 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 5USJ · PDBe 5USJ · UniProt P01116
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