MolNFT v1 · #145045 · protein
NMR data-driven model of GTPase KRAS-gmppnp tethered to a nanodisc (E3 state)
6CCH · Apolipoprotein a-I: “NMR data-driven model of GTPase KRAS-gmppnp tethered to a nanodisc (E3 state)”. Solution nmr, 4 ligands (PCW, 17F, GNP), 3 pockets (best druggability 0.51). MolNFT v1 #145045 on GenesisL1: 3D structure, binding…
- PDB
- 6CCH
- Type
- protein
- Length
- 581 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apolipoprotein a-I; GTPase KRAS
- UniProt
- P02647, P01116
- Ligands
- PCW, 17F, GNP, MG
- Pockets
- 3 · best druggability 0.51
Structure
solution nmr · 2 distinct chains · 67% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Apolipoprotein a-I | protein | 198 | 98% helix, 0% strand | P02647 |
| B | GTPase KRAS | protein | 185 | 34% helix, 24% strand | P01116 |
Ligands and binding sites
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 64 copies · chains C, A, B
- 17F · O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine · ligand · 16 copies · chains A, B, C
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains B
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.51 | 0.79 | 30 | GNP |
| 2 | 51 | 0.39 | 0.81 | 14 | empty |
| 3 | 57 | 0.28 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–C · 3975 Ų buried · 68 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6CCH · NMR data-driven model of GTPase KRas-GMPPNP tethered to a nanodisc (E3 state) · 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 6CCH · PDBe 6CCH · UniProt P02647 · UniProt P01116
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