MolNFT v1 · #38702 · protein
W102T/Y365F protein farnesyltransferase double mutant complexed with a geranylgeranylated ddptasacvls peptide product at 3.0A
2H6I · Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type…: “W102T/Y365F protein farnesyltransferase double mutant complexed with a geranylgeranylated ddptasacvls peptide…”. X-ray diffraction, 4 ligands (GER, GLC, FRU), 11 pockets…
- PDB
- 2H6I
- Type
- protein
- Length
- 729 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type I alpha subunit; Protein…
- EC
- 2.5.1.58, 2.5.1.59
- UniProt
- P49354, P49356
- Ligands
- GER, GLC, FRU, ZN
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type I alpha subunit (EC 2.5.1.58, 2.5.1.59) | protein | 315 | 70% helix, 1% strand | P49354 |
| B | Protein farnesyltransferase beta subunit (EC 2.5.1.58) | protein | 410 | 49% helix, 7% strand | P49356 |
| P | Farnesylated peptide | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- GER · Geran-8-yl geran · ligand · chains A, B, P
- GLC · alpha-D-glucopyranose · sugar · chains A, B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- ZN · Zinc ion · metal · chains B, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 971 | 0.86 | 0.88 | 119 | GER |
| 2 | 248 | 0.64 | 0.82 | 27 | empty |
| 3 | 235 | 0.54 | 0.77 | 32 | empty |
| 4 | 127 | 0.52 | 0.81 | 31 | empty |
| 5 | 76 | 0.45 | 0.82 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3497 Ų buried · 69 hydrogen bonds · protein-protein
- B–P · 260 Ų buried · 1 hydrogen bond · protein-protein
- A–P · 133 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 lipid (geranylgeranylation).
Compared structures
- 2H6I · W102T/Y365F Protein Farnesyltransferase Double Mutant Complexed with a Geranylgeranylated… · the same entry in another collection · chain A against A, TM-score 1.00
- P49356 · AlphaFold monomer V2.0 prediction for protein farnesyltransferase subunit beta (P49356) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P49354 · AlphaFold monomer V2.0 prediction for protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERAS… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P49354
- Every structure of UniProt P49356
- Elsewhere: RCSB PDB 2H6I · PDBe 2H6I · UniProt P49354 · UniProt P49356
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