Research workbench
Antibody derived (abd-7) small molecule binding to KRAS.
Analyse Antibody derived (abd-7) small molecule binding to KRAS. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FA4
- Type
- protein
- Length
- 1,018 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GNP, D1W, MG
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | GTPase KRAS | protein | 173 | 38% helix, 26% strand | P01116 |
| A | GTPase KRAS | protein | 172 | 37% helix, 26% strand | P01116 |
| C, E | GTPase KRAS | protein | 169 | 38% helix, 27% strand | P01116 |
| D | GTPase KRAS | protein | 167 | 37% helix, 27% strand | P01116 |
| F | GTPase KRAS | protein | 168 | 37% helix, 27% strand | P01116 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains B, A, C, D, E, F
- D1W · 6-(2,3-dihydro-1,4-benzodioxin-5-yl)-~{N}-[4-[(dimethylamino)methyl]phenyl]-2-methoxy-pyridin-3-amine · ligand · 5 copies · chains B, E, A, C, D, F
- MG · Magnesium ion · metal · 6 copies · chains B, A, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.81 | 0.82 | 140 | empty |
| 2 | 948 | 0.80 | 0.82 | 106 | empty |
| 3 | 197 | 0.59 | 0.81 | 32 | GNP, MG |
| 4 | 185 | 0.58 | 0.81 | 30 | MG, GNP |
| 5 | 185 | 0.58 | 0.81 | 28 | MG, GNP |
Interfaces
12 interfaces between chains.
- A–C · 657 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 631 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 618 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 365 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 363 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6FA4 · Antibody derived (Abd-7) small molecule binding to KRAS. · the same entry in another collection · chain B against B, 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
- Elsewhere: RCSB PDB 6FA4 · PDBe 6FA4 · UniProt P01116
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.