MolNFT v1 · #118079 · protein
Crystal structure of cyclization domain of phomopsis amygdali fusicoccadiene synthase complexed with manganese ions and neridronate
5ER8: “Crystal structure of cyclization domain of phomopsis amygdali fusicoccadiene synthase complexed with…”. X-ray diffraction, 3 ligands (NRD, MN, CL), 8 pockets (best druggability 0.83). MolNFT v1 #118079 on GenesisL1: 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.