Research workbench
Protein farnesyltransferase complexed with a RAP2A peptide substrate and a fpp analog at 1.8A resolution
Analyse Protein farnesyltransferase complexed with a RAP2A peptide substrate and a fpp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TN6
- Type
- protein
- Length
- 736 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein farnesyltransferase alpha subunit; Protein farnesyltransferase beta subunit…
- EC
- 2.5.1.58
- UniProt
- P49354, P49356
- Ligands
- FII, GLC, FRU, ZN
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 58% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein farnesyltransferase alpha subunit (EC 2.5.1.58) | protein | 315 | 69% helix, 1% strand | P49354 |
| B | Protein farnesyltransferase beta subunit (EC 2.5.1.58) | protein | 410 | 50% helix, 7% strand | P49356 |
| C | Peptide derived from the C-terminus of RAP2A | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- FII · [(3,7,11-trimethyl-dodeca-2,6,10-trienyloxycarbamoyl)-methyl]-phosphonic acid · ligand · chains A, B, C
- GLC · alpha-D-glucopyranose · sugar · chains A, B
- FRU · beta-D-fructofuranose · sugar · chains A, B
- ZN · Zinc ion · metal · chains B, C
- ACY · Acetic acid · additive · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 533 | 0.80 | 0.86 | 71 | empty |
| 2 | 469 | 0.78 | 0.86 | 60 | FII |
| 3 | 210 | 0.67 | 0.85 | 39 | empty |
| 4 | 255 | 0.64 | 0.81 | 32 | ACY |
| 5 | 230 | 0.53 | 0.76 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3520 Ų buried · 75 hydrogen bonds · protein-protein
- B–C · 602 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 201 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1TN6 · Protein Farnesyltransferase Complexed with a Rap2a Peptide Substrate and a FPP Analog at… · 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 1TN6 · PDBe 1TN6 · UniProt P49354 · UniProt P49356
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