MolNFT v1 · #121512 · protein
Crystal structure of Z,Z-farnesyl diphosphate synthase (D71M, E75A and H103Y mutants) complexed with ipp and dmspp
5HXT · (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic: “Crystal structure of Z,Z-farnesyl diphosphate synthase (D71M, E75A and H103Y mutants) complexed with ipp and…”. X-ray diffraction, 4 ligands (DST, IPR, O4B), 3 pockets (best…
- PDB
- 5HXT
- Type
- protein
- Length
- 447 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic
- EC
- 2.5.1.92
- UniProt
- B8XA40
- Ligands
- DST, IPR, O4B, MG
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic (EC 2.5.1.92) | protein | 221 | 50% helix, 15% strand | B8XA40 |
| B | (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic (EC 2.5.1.92) | protein | 226 | 49% helix, 15% strand | B8XA40 |
Ligands and binding sites
- DST · Dimethylallyl S-thiolodiphosphate · ligand · 2 copies · chains A, B
- IPR · Isopentyl pyrophosphate · ligand · 2 copies · chains A, B
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.66 | 0.83 | 31 | MG, DST, IPR |
| 2 | 343 | 0.66 | 0.81 | 42 | MG, DST, IPR |
| 3 | 50 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1789 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5HXT · Crystal Structure of Z,Z-Farnesyl Diphosphate Synthase (D71M, E75A and H103Y Mutants)… · the same entry in another collection · chain A against A, TM-score 1.00
- B8XA40 · AlphaFold monomer V2.0 prediction for (2Z,6Z)-farnesyl diphosphate synthase… · 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 B8XA40
- Elsewhere: RCSB PDB 5HXT · PDBe 5HXT · UniProt B8XA40
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