MolNFT v1 · #158422 · protein
Crystal structure of G12V HRAS-gppnhp bound in complex with the engineered rbd variant 12 of craf kinase protein
6NTD · GTPase HRAS: “Crystal structure of G12V HRAS-gppnhp bound in complex with the engineered rbd variant 12 of craf kinase…”. X-ray diffraction, 2 ligands (GNP, MG), 3 pockets (best druggability 0.65). MolNFT v1 #158422 on GenesisL1: 3D…
- PDB
- 6NTD
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS; RAF proto-oncogene SERINE/THREONINE-protein kinase
- EC
- 2.7.11.1
- UniProt
- P01112, P04049
- Ligands
- GNP, MG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRAS | protein | 167 | 38% helix, 28% strand | P01112 |
| B | RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 64 | 22% helix, 28% strand | P04049 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.65 | 0.85 | 35 | empty |
| 2 | 174 | 0.49 | 0.77 | 35 | MG, GNP |
| 3 | 127 | 0.45 | 0.77 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 555 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6NTD · Crystal Structure of G12V HRas-GppNHp bound in complex with the engineered RBD variant 12… · 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 0.90
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 P01112
- Every structure of UniProt P04049
- Elsewhere: RCSB PDB 6NTD · PDBe 6NTD · UniProt P01112 · UniProt P04049
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