Research workbench
Crystal structure of KRAS4B (gmppnp-bound) in complex with the rbd-pH domains of SIN1
Analyse Crystal structure of KRAS4B (gmppnp-bound) in complex with the rbd-pH domains… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LC1
- Type
- protein
- Length
- 766 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 2B of GTPase KRAS; Target of rapamycin complex 2 subunit MAPKAP1
- EC
- 3.6.5.2
- UniProt
- P01116, Q9BPZ7
- Ligands
- GNP, MG
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 167 | 39% helix, 28% strand | P01116 |
| B | Target of rapamycin complex 2 subunit MAPKAP1 | protein | 218 | 22% helix, 38% strand | Q9BPZ7 |
| C | Isoform 2B of GTPase KRAS (EC 3.6.5.2) | protein | 167 | 38% helix, 26% strand | P01116 |
| D | Target of rapamycin complex 2 subunit MAPKAP1 | protein | 214 | 17% helix, 39% strand | Q9BPZ7 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.68 | 0.85 | 26 | empty |
| 2 | 280 | 0.66 | 0.82 | 28 | empty |
| 3 | 185 | 0.65 | 0.85 | 36 | MG, GNP |
| 4 | 214 | 0.65 | 0.84 | 37 | MG, GNP |
| 5 | 250 | 0.49 | 0.74 | 25 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1097 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1038 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 99 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 21 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7LC1 · Crystal Structure of KRAS4b (GMPPNP-bound) in complex with the RBD-PH domains of SIN1 · 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 B against A, TM-score 0.60
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 7LC1 · PDBe 7LC1 · UniProt P01116 · UniProt Q9BPZ7
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