Research workbench
Crystal structure of G12V HRAS-gppnhp bound in complex with the engineered rbd variant 1 of craf kinase protein
Analyse Crystal structure of G12V HRAS-gppnhp bound in complex with the engineered rbd… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NTC
- 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 0.73
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRAS | protein | 168 | 36% helix, 28% strand | P01112 |
| B | RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 63 | 24% helix, 29% strand | P04049 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.73 | 0.85 | 49 | empty |
| 2 | 169 | 0.58 | 0.82 | 38 | GNP, MG |
| 3 | 67 | 0.42 | 0.80 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 471 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6NTC · Crystal Structure of G12V HRas-GppNHp bound in complex with the engineered RBD variant 1… · 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 0.91
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 6NTC · PDBe 6NTC · UniProt P01112 · UniProt P04049
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