MolNFT v1 · #168067 · protein
NMR-driven structure of KRAS4B-GDP homodimer on a lipid bilayer nanodisc
6W4F · Apolipoprotein a-I: “NMR-driven structure of KRAS4B-GDP homodimer on a lipid bilayer nanodisc”. Solution nmr, 4 ligands (PCW, 17F, GDP), 8 pockets (best druggability 0.71). MolNFT v1 #168067 on GenesisL1: 3D structure, binding sites…
- PDB
- 6W4F
- Type
- protein
- Length
- 756 residues
- Chains
- 4
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apolipoprotein a-I; GTPase KRAS
- UniProt
- P02647, P01116
- Ligands
- PCW, 17F, GDP, MG
- Pockets
- 8 · best druggability 0.71
Structure
solution nmr · 2 distinct chains · 69% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Apolipoprotein a-I | protein | 198 | 97% helix, 0% strand | P02647 |
| B, C | GTPase KRAS | protein | 180 | 38% helix, 22% strand | P01116 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 64 copies · chains A, B, C, D
- 17F · O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine · ligand · 16 copies · chains B, D, C
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains B, C
- MG · Magnesium ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.71 | 0.98 | 21 | empty |
| 2 | 410 | 0.70 | 0.82 | 52 | empty |
| 3 | 85 | 0.66 | 0.92 | 20 | empty |
| 4 | 252 | 0.65 | 0.82 | 39 | empty |
| 5 | 190 | 0.52 | 0.78 | 33 | GDP |
Interfaces
2 interfaces between chains.
- A–D · 3726 Ų buried · 54 hydrogen bonds · protein-protein
- B–C · 1103 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6W4F · NMR-driven structure of KRAS4B-GDP homodimer on a lipid bilayer nanodisc · the same entry in another collection · chain A against A, TM-score 1.00
- P02647 · AlphaFold monomer V2.0 prediction for apolipoprotein a-I (P02647) · a predicted model of the same protein · chain A against A, TM-score 0.58
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 P02647
- Every structure of UniProt P01116
- Elsewhere: RCSB PDB 6W4F · PDBe 6W4F · UniProt P02647 · UniProt P01116
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