MolNFT v1 · #118092 · protein
Crystal structure of cyclization domain of phomopsis amygdali fusicoccadiene synthase complexed with magnesium ions and pamidronate
5ERM: “Crystal structure of cyclization domain of phomopsis amygdali fusicoccadiene synthase complexed with…”. X-ray diffraction, 3 ligands (210, MG, CL), 6 pockets (best druggability 0.79). MolNFT v1 #118092 on GenesisL1: 3D structure…
- PDB
- 5ERM
- Type
- protein
- Length
- 615 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
- 210, MG, CL
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusicoccadiene synthase (EC 4.2.3.43) | protein | 301 | 60% helix, 2% strand | A2PZA5 |
| B | Fusicoccadiene synthase (EC 4.2.3.43) | protein | 314 | 62% helix, 2% strand | A2PZA5 |
Ligands and binding sites
- 210 · Pamidronate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.79 | 0.82 | 74 | 210, MG |
| 2 | 698 | 0.78 | 0.82 | 66 | MG, 210 |
| 3 | 869 | 0.76 | 0.79 | 73 | empty |
| 4 | 149 | 0.52 | 0.80 | 19 | empty |
| 5 | 132 | 0.51 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 623 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5ERM · 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 5ERM · PDBe 5ERM · UniProt A2PZA5
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