Research workbench
Crystal structure of Z,Z-farnesyl diphosphate synthase (D71M, E75A and H103Y mutants) complexed with ipp
Analyse Crystal structure of Z,Z-farnesyl diphosphate synthase (D71M, E75A and H103Y… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HXP
- 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
- IPR, O4B, MG
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic (EC 2.5.1.92) | protein | 224 | 48% helix, 15% strand | B8XA40 |
| C | (2Z,6Z)-farnesyl diphosphate synthase, chloroplastic (EC 2.5.1.92) | protein | 223 | 48% helix, 15% strand | B8XA40 |
Ligands and binding sites
- IPR · Isopentyl pyrophosphate · ligand · 3 copies · chains A, C
- O4B · 1,4,7,10,13,16-hexaoxacyclooctadecane · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · chains A, C
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 | 176 | 0.79 | 0.94 | 30 | MG, IPR |
| 2 | 173 | 0.58 | 0.81 | 23 | IPR |
| 3 | 50 | 0.29 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 1971 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 5HXP · 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 C 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 5HXP · PDBe 5HXP · UniProt B8XA40
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