MolNFT v1 · #180819 · protein
Crystal structure of KRAS4B-Q61R (gmppnp-bound) in complex with the RAS-binding domain (rbd) of SIN1
7LC2 · GTPase KRAS: “Crystal structure of KRAS4B-Q61R (gmppnp-bound) in complex with the RAS-binding domain (rbd) of SIN1”. X-ray diffraction, 2 ligands (GNP, MG), 5 pockets (best druggability 0.69). MolNFT v1 #180819 on GenesisL1: 3D…
- PDB
- 7LC2
- Type
- protein
- Length
- 482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS; Target of rapamycin complex 2 subunit MAPKAP1
- EC
- 3.6.5.2
- UniProt
- P01116, Q9BPZ7
- Ligands
- GNP, MG
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRAS (EC 3.6.5.2) | protein | 167 | 36% helix, 27% strand | P01116 |
| B | GTPase KRAS (EC 3.6.5.2) | protein | 166 | 37% helix, 27% strand | P01116 |
| D | Target of rapamycin complex 2 subunit MAPKAP1 | protein | 76 | 21% helix, 32% strand | Q9BPZ7 |
| E | Target of rapamycin complex 2 subunit MAPKAP1 | protein | 73 | 16% helix, 34% strand | Q9BPZ7 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.69 | 0.83 | 37 | GNP, MG |
| 2 | 258 | 0.68 | 0.84 | 37 | GNP, MG |
| 3 | 315 | 0.61 | 0.79 | 38 | empty |
| 4 | 55 | 0.33 | 0.77 | 13 | empty |
| 5 | 60 | 0.28 | 0.73 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–E · 614 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 609 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 383 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 174 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 7LC2 · Crystal Structure of KRAS4b-Q61R (GMPPNP-bound) in complex with the RAS-binding domain… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BPZ7 · AlphaFold monomer V2.0 prediction for target of rapamycin complex 2 subunit MAPKAP1… · a predicted model of the same protein · chain D 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 P01116
- Every structure of UniProt Q9BPZ7
- Elsewhere: RCSB PDB 7LC2 · PDBe 7LC2 · UniProt P01116 · UniProt Q9BPZ7
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