Research workbench
Crystal structure of wild-type KRAS4B(1-169) in complex with gmppnp and mg ion
Analyse Crystal structure of wild-type KRAS4B(1-169) in complex with gmppnp and mg ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VC8
- Type
- protein
- Length
- 470 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GNP, MG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 160 | 37% helix, 27% strand | P01116 |
| B | GTPase KRAS | protein | 160 | 37% helix, 26% strand | P01116 |
| C | GTPase KRAS | protein | 150 | 39% helix, 27% strand | P01116 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.67 | 0.75 | 50 | empty |
| 2 | 169 | 0.53 | 0.79 | 30 | GNP, MG |
| 3 | 162 | 0.51 | 0.79 | 29 | GNP, MG |
| 4 | 158 | 0.43 | 0.75 | 23 | GNP |
Interfaces
2 interfaces between chains.
- A–C · 321 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 276 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6VC8 · Crystal structure of wild-type KRAS4b(1-169) in complex with GMPPNP and Mg ion · 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 6VC8 · PDBe 6VC8 · UniProt P01116
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