MolNFT v1 · #93137 · protein
Ftase in complex with bms analogue 11
4GTM · Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type…: “Ftase in complex with bms analogue 11”. X-ray diffraction, 3 ligands (FPP, 7TM, ZN), 11 pockets (best druggability 0.81). MolNFT v1 #93137 on GenesisL1: 3D structure…
- PDB
- 4GTM
- Type
- protein
- Length
- 723 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type- 1 subunit alpha; Protein…
- EC
- 2.5.1.58, 2.5.1.59
- UniProt
- Q04631, Q02293
- Ligands
- FPP, 7TM, ZN
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERASE type- 1 subunit alpha (EC 2.5.1.58, 2.5.1.59) | protein | 318 | 69% helix, 1% strand | Q04631 |
| B | Protein farnesyltransferase subunit beta (EC 2.5.1.58) | protein | 405 | 52% helix, 7% strand | Q02293 |
Ligands and binding sites
- FPP · Farnesyl diphosphate · ligand · chains A, B
- 7TM · 4-({(3R)-7-cyano-4-[(4-methoxyphenyl)sulfonyl]-1-[(1-methyl-1H-imidazol-5-yl)methyl]-2,3,4,5-tetrahydro-1H-1,4-benzodiazepin-3-yl}methyl)phenyl hexylcarbamate · ligand · chains A, B
- ZN · Zinc ion · metal · chains B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.81 | 0.82 | 98 | FPP, 7TM, DMS |
| 2 | 234 | 0.71 | 0.86 | 36 | empty |
| 3 | 68 | 0.52 | 0.86 | 17 | empty |
| 4 | 164 | 0.45 | 0.75 | 20 | empty |
| 5 | 128 | 0.44 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 3546 Ų buried · 69 hydrogen bonds · protein-protein
Compared structures
- 4GTM · FTase in complex with BMS analogue 11 · the same entry in another collection · chain A against A, TM-score 1.00
- Q04631 · AlphaFold monomer V2.0 prediction for protein FARNESYLTRANSFERASE/GERANYLGERANYLTRANSFERAS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q02293 · AlphaFold monomer V2.0 prediction for protein farnesyltransferase subunit beta (Q02293) · a predicted model of the same protein · chain B 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 Q04631
- Every structure of UniProt Q02293
- Elsewhere: RCSB PDB 4GTM · PDBe 4GTM · UniProt Q04631 · UniProt Q02293
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