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Crystal structure of cyclization domain of phomopsis amygdali fusicoccadiene synthase complexed with manganese ions and neridronate
Analyse Crystal structure of cyclization domain of phomopsis amygdali fusicoccadiene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ER8
- Type
- protein
- Length
- 598 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusicoccadiene synthase
- EC
- 4.2.3.43
- UniProt
- A2PZA5
- Ligands
- NRD, MN, CL
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 62% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusicoccadiene synthase (EC 4.2.3.43) | protein | 294 | 61% helix, 2% strand | A2PZA5 |
| B | Fusicoccadiene synthase (EC 4.2.3.43) | protein | 304 | 63% helix, 2% strand | A2PZA5 |
Ligands and binding sites
- NRD · (6-azanyl-1-oxidanyl-1-phosphono-hexyl)phosphonic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 9 copies · chains A, B
- CL · Chloride ion · ion · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.83 | 0.84 | 91 | NRD |
| 2 | 401 | 0.75 | 0.85 | 41 | NRD |
| 3 | 174 | 0.55 | 0.80 | 23 | empty |
| 4 | 152 | 0.53 | 0.80 | 22 | empty |
| 5 | 111 | 0.53 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 558 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5ER8 · Crystal structure of cyclization domain of Phomopsis amygdali fusicoccadiene synthase… · the same entry in another collection · chain A against A, TM-score 1.00
- A2PZA5 · AlphaFold monomer V2.0 prediction for fusicoccadiene synthase (A2PZA5) · 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 A2PZA5
- Elsewhere: RCSB PDB 5ER8 · PDBe 5ER8 · UniProt A2PZA5
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