Research workbench
KRAS-169 Q61H gppnhp + ppin-1
Analyse KRAS-169 Q61H gppnhp + ppin-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GOM
- Type
- protein
- Length
- 984 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.63
- Source
- Homo sapiens
- Molecule
- GTPase KRas
- UniProt
- P01116
- Ligands
- GNP, F6E, MG, PO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.63 · 6 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase KRas | protein | 171 | 37% helix, 26% strand | P01116 |
| B | GTPase KRas | protein | 169 | 37% helix, 27% strand | P01116 |
| C | GTPase KRas | protein | 160 | 38% helix, 26% strand | P01116 |
| D | GTPase KRas | protein | 161 | 38% helix, 27% strand | P01116 |
| E | GTPase KRas | protein | 163 | 36% helix, 28% strand | P01116 |
| F | GTPase KRas | protein | 160 | 38% helix, 26% strand | P01116 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- F6E · (6~{S})-1-(1~{H}-imidazol-4-ylcarbonyl)-6-[(4-phenylphenyl)methyl]-4-propyl-1,4-diazepan-5-one · ligand · chains A, C
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- PO4 · Phosphate ion · ion · chains A, B, D
- CIT · Citric acid · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.81 | 0.82 | 115 | PO4 |
| 2 | 682 | 0.78 | 0.83 | 86 | empty |
| 3 | 226 | 0.61 | 0.81 | 31 | GNP, MG |
| 4 | 233 | 0.58 | 0.79 | 29 | GNP, MG |
| 5 | 162 | 0.56 | 0.81 | 23 | empty |
Interfaces
12 interfaces between chains.
- B–E · 619 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 549 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 361 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 353 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (oxidation).
Compared structures
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
- Elsewhere: RCSB PDB 6GOM · PDBe 6GOM · UniProt P01116
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