MolNFT v1 · #118094 · protein
Crystal structure of elongation domain of phomopsis amygdali fusicoccadiene synthase complexed with cobalt ions and pamidronate
5ERO: “Crystal structure of elongation domain of phomopsis amygdali fusicoccadiene synthase complexed with cobalt…”. X-ray diffraction, 2 ligands (210, CO), 9 pockets (best druggability 0.83). MolNFT v1 #118094 on GenesisL1: 3D structure…
- PDB
- 5ERO
- Type
- protein
- Length
- 900 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fusicoccadiene synthase
- EC
- 2.5.1.29
- UniProt
- A2PZA5
- Ligands
- 210, CO
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fusicoccadiene synthase (EC 2.5.1.29) | protein | 301 | 76% helix, 1% strand | A2PZA5 |
| B | Fusicoccadiene synthase (EC 2.5.1.29) | protein | 300 | 76% helix, 1% strand | A2PZA5 |
| C | Fusicoccadiene synthase (EC 2.5.1.29) | protein | 299 | 73% helix, 1% strand | A2PZA5 |
Ligands and binding sites
- 210 · Pamidronate · ligand · 3 copies · chains A, B, C
- CO · Cobalt (II) ion · metal · 12 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.83 | 0.90 | 49 | CO, 210 |
| 2 | 555 | 0.82 | 0.88 | 56 | CO, 210 |
| 3 | 558 | 0.82 | 0.87 | 54 | CO, 210 |
| 4 | 473 | 0.67 | 0.79 | 54 | empty |
| 5 | 181 | 0.59 | 0.82 | 31 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1838 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 539 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 487 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5ERO · Crystal structure of elongation 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 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 A2PZA5
- Elsewhere: RCSB PDB 5ERO · PDBe 5ERO · UniProt A2PZA5
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