Research workbench
Crystal structure of G13D-KRAS (gmppnp-bound) in complex with gap- related domain (grd) of neurofibromin (NF1)
Analyse Crystal structure of G13D-KRAS (gmppnp-bound) in complex with gap- related… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OB3
- Type
- protein
- Length
- 828 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; Neurofibromin
- UniProt
- P01116, P21359
- Ligands
- GNP, MG, CL
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS | protein | 170 | 40% helix, 27% strand | P01116 |
| B | Neurofibromin | protein | 245 | 75% helix, 0% strand | P21359 |
| C | GTPase KRAS | protein | 166 | 39% helix, 28% strand | P01116 |
| D | Neurofibromin | protein | 247 | 74% helix, 0% strand | P21359 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 3 copies · chains B, C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 5 copies · chains B, D, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 519 | 0.74 | 0.83 | 67 | GNP, MG |
| 2 | 1119 | 0.72 | 0.76 | 89 | MES, CL |
| 3 | 75 | 0.72 | 0.96 | 18 | empty |
| 4 | 248 | 0.67 | 0.84 | 36 | GNP, MG |
| 5 | 291 | 0.65 | 0.81 | 42 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1433 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1365 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 323 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 281 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6OB3 · Crystal structure of G13D-KRAS (GMPPNP-bound) in complex with GAP-related domain (GRD) of… · the same entry in another collection · chain A against A, TM-score 1.00
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 P21359
- Elsewhere: RCSB PDB 6OB3 · PDBe 6OB3 · UniProt P01116 · UniProt P21359
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