MolNFT v1 · #148556 · protein
Antibody derived (abd-6) small molecule binding to KRAS.
6FA3 · GTPase KRAS: “Antibody derived (abd-6) small molecule binding to KRAS.”. X-ray diffraction, 3 ligands (GNP, D1Z, MG), 15 pockets (best druggability 0.81). MolNFT v1 #148556 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6FA3
- Type
- protein
- Length
- 1,017 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GNP, D1Z, MG
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D | GTPase KRAS | protein | 172 | 38% helix, 26% strand | P01116 |
| A | GTPase KRAS | protein | 171 | 37% helix, 26% strand | P01116 |
| C | GTPase KRAS | protein | 170 | 38% helix, 26% strand | P01116 |
| E | GTPase KRAS | protein | 167 | 37% helix, 27% strand | P01116 |
| F | GTPase KRAS | protein | 165 | 36% helix, 27% strand | P01116 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains B, A, C, D, E, F
- D1Z · ~{N}-[[(3~{R})-5-[5-[[3-[(dimethylamino) methyl]phenyl]amino]-6-methoxy-pyridin-2-yl]-2,3-dihydro-1,4-benzodioxin-3-yl]methyl]oxane-4-carboxamide · ligand · 4 copies · chains B, E, A, C, D, F
- MG · Magnesium ion · metal · 6 copies · chains B, A, C, D, E, F
- DMS · Dimethyl sulfoxide · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.81 | 0.82 | 134 | empty |
| 2 | 1011 | 0.81 | 0.82 | 121 | empty |
| 3 | 429 | 0.66 | 0.79 | 52 | MG, GNP |
| 4 | 183 | 0.59 | 0.82 | 31 | MG, GNP |
| 5 | 187 | 0.58 | 0.81 | 29 | MG, GNP |
Interfaces
12 interfaces between chains.
- B–E · 642 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 638 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 600 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 366 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 366 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 modified (oxidation).
Compared structures
- 6FA3 · Antibody derived (Abd-6) 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 6FA3 · PDBe 6FA3 · UniProt P01116
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