Research workbench
Crystal structure of leshmaniasis major farnesyl diphosphate synthase in complex with 1-(2-hydroxy-2,2-diphosphonoethyl)-3- phenylpyridinium, ipp and CA2+
Analyse Crystal structure of leshmaniasis major farnesyl diphosphate synthase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JZB
- Type
- protein
- Length
- 724 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Farnesyl pyrophosphate synthase
- EC
- 2.5.1.1, 2.5.1.10
- UniProt
- Q4QBL1
- Ligands
- IPE, P2H, CA, NA
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Farnesyl pyrophosphate synthase (EC 2.5.1.1, 2.5.1.10) | protein | 362 | 73% helix, 1% strand | Q4QBL1 |
Ligands and binding sites
- IPE · 3-methylbut-3-enyl trihydrogen diphosphate · ligand · 2 copies · chains A, B
- P2H · 1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 385 | 0.83 | 0.92 | 58 | CA, IPE, P2H |
| 2 | 378 | 0.83 | 0.92 | 59 | IPE, P2H, CA |
| 3 | 187 | 0.53 | 0.79 | 26 | empty |
| 4 | 141 | 0.53 | 0.81 | 26 | empty |
| 5 | 196 | 0.50 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2955 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (formylation).
Compared structures
- 4JZB · Crystal Structure of Leshmaniasis major Farnesyl diphosphate synthase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q4QBL1
- Elsewhere: RCSB PDB 4JZB · PDBe 4JZB · UniProt Q4QBL1
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