Research workbench
Crystal structure of Q61L KRAS(GMPPNP)-NF1(GRD)-SPRED1(EVH1) complex
Analyse Crystal structure of Q61L KRAS(GMPPNP)-NF1(GRD)-SPRED1(EVH1) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V6F
- Type
- protein
- Length
- 579 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
- 8 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sprouty-related, EVH1 domain-containing protein 1 | protein | 110 | 15% helix, 51% strand | Q7Z699 |
| B | Neurofibromin | protein | 301 | 66% helix, 0% strand | P21359 |
| C | GTPase KRAS | protein | 168 | 39% helix, 26% 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
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.75 | 0.80 | 87 | GNP, MG |
| 2 | 209 | 0.69 | 0.85 | 34 | empty |
| 3 | 167 | 0.58 | 0.82 | 22 | empty |
| 4 | 256 | 0.56 | 0.77 | 26 | FMT |
| 5 | 218 | 0.52 | 0.77 | 30 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1178 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 880 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6V6F · Crystal structure of Q61L KRAS(GMPPNP)-NF1(GRD)-SPRED1(EVH1) 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 6V6F · PDBe 6V6F · UniProt Q7Z699 · UniProt P21359 · UniProt P01116
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