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Crystal structure of cyclization domain of phomopsis amygdali fusicoccadiene synthase complexed with magnesium ions and pamidronate
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
- 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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