MolNFT v1 · #101212 · protein
The effects of lysine 200 and phenylalanine 239 farnesyl pyrophosphate synthase (fpps) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates
4NKE: “The effects of lysine 200 and phenylalanine 239 farnesyl pyrophosphate synthase (fpps) mutations on the…”. X-ray diffraction, 3 ligands (RIS, IPE, MG), 3 pockets (best druggability 0.80). MolNFT v1 #101212 on GenesisL1: 3D…
- PDB
- 4NKE
- Type
- protein
- Length
- 338 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- EC
- 2.5.1.10, 2.5.1.1
- UniProt
- P14324
- Ligands
- RIS, IPE, MG
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Farnesyl pyrophosphate synthase (EC 2.5.1.10, 2.5.1.1) | protein | 338 | 76% helix, 1% strand | P14324 |
Ligands and binding sites
- RIS · 1-hydroxy-2-(3-pyridinyl)ethylidene bis-phosphonic acid · ligand · chains A
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
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 | 475 | 0.80 | 0.87 | 50 | MG, RIS, IPE, EDO |
| 2 | 98 | 0.43 | 0.78 | 18 | empty |
| 3 | 53 | 0.31 | 0.76 | 15 | empty |
Compared structures
- 4NKE · The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS)… · the same entry in another collection · chain A against A, TM-score 1.00
- P14324 · AlphaFold monomer V2.0 prediction for farnesyl pyrophosphate synthase (P14324) · 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 P14324
- Elsewhere: RCSB PDB 4NKE · PDBe 4NKE · UniProt P14324
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