Research workbench
Crystal structure of KRAS-G13D (gmppnp-bound) in complex with RAS- binding domain (rbd) and cysteine-rich domain (crd) of RAF1/CRAF
Analyse Crystal structure of KRAS-G13D (gmppnp-bound) in complex with RAS- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XGV
- Type
- protein
- Length
- 302 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; RAF proto-oncogene SERINE/THREONINE-protein kinase
- EC
- 3.6.5.2, 2.7.11.1
- UniProt
- P01116, P04049
- Ligands
- GNP, ZN, MG, CL
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS (EC 3.6.5.2) | protein | 168 | 40% helix, 26% strand | P01116 |
| B | RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 134 | 17% helix, 36% strand | P04049 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.68 | 0.80 | 50 | GNP, MG |
| 2 | 57 | 0.37 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1229 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 6XGV · Crystal Structure of KRAS-G13D (GMPPNP-bound) in complex with RAS-binding domain (RBD)… · the same entry in another collection · chain A against A, TM-score 1.00
- P04049 · AlphaFold monomer V2.0 prediction for RAF proto-oncogene SERINE/THREONINE-protein kinase… · a predicted model of the same protein · chain B against A, TM-score 0.76
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
- Every structure of UniProt P04049
- Elsewhere: RCSB PDB 6XGV · PDBe 6XGV · UniProt P01116 · UniProt P04049
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