MolNFT v1 · #166946 · protein
Crystal structure of KRAS(GMPPNP)-NF1(GRD)-SPRED1 complex
6V65 · Sprouty-related, EVH1 domain-containing protein 1: “Crystal structure of KRAS(GMPPNP)-NF1(GRD)-SPRED1 complex”. X-ray diffraction, 3 ligands (GNP, ZN, MG), 6 pockets (best druggability 0.77). MolNFT v1 #166946 on GenesisL1: 3D…
- PDB
- 6V65
- Type
- protein
- Length
- 578 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sprouty-related, EVH1 domain-containing protein 1; Neurofibromin; GTPase KRAS
- UniProt
- Q7Z699, P21359, P01116
- Ligands
- GNP, ZN, MG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sprouty-related, EVH1 domain-containing protein 1 | protein | 110 | 15% helix, 52% strand | Q7Z699 |
| B | Neurofibromin | protein | 300 | 63% helix, 0% strand | P21359 |
| C | GTPase KRAS | protein | 168 | 40% helix, 28% strand | P01116 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains C
- ZN · Zinc ion · metal · chains A
- MG · Magnesium ion · metal · chains C
- FMT · Formic acid · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.77 | 0.79 | 107 | GNP, MG |
| 2 | 227 | 0.70 | 0.86 | 34 | empty |
| 3 | 295 | 0.61 | 0.79 | 40 | FMT |
| 4 | 105 | 0.45 | 0.79 | 29 | empty |
| 5 | 122 | 0.44 | 0.77 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1220 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 923 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6V65 · Crystal structure of KRAS(GMPPNP)-NF1(GRD)-SPRED1 complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q7Z699 · AlphaFold monomer V2.0 prediction for sprouty-related, EVH1 domain- containing protein 1… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q7Z699
- Every structure of UniProt P21359
- Every structure of UniProt P01116
- Elsewhere: RCSB PDB 6V65 · PDBe 6V65 · UniProt Q7Z699 · UniProt P21359 · UniProt P01116
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