MolNFT v1 · #16939 · protein
Isopenicillin N synthase from aspergillus nidulans (oxygen-exposed product from anaerobic ac-vinylglycine fe complex)
1ODN: “Isopenicillin N synthase from aspergillus nidulans (oxygen-exposed product from anaerobic ac-vinylglycine fe…”. X-ray diffraction, 3 ligands (APV, FE2, SO4), 2 pockets (best druggability 0.70). MolNFT v1 #16939 on GenesisL1: 3D…
- PDB
- 1ODN
- Type
- protein
- Length
- 321 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopenicillin N synthase
- UniProt
- P05326
- Ligands
- APV, FE2, SO4
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopenicillin N synthase | protein | 321 | 29% helix, 21% strand | P05326 |
Ligands and binding sites
- APV · 6-(5-amino-5-carboxy-pentanoylamino)-3-hydroxymethyl-7-oxo-4-thia-1-aza-bicyclo[3.2.0]heptane-2-carboxylic acid · ligand · chains A
- FE2 · Fe (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.70 | 0.79 | 38 | APV |
| 2 | 99 | 0.35 | 0.74 | 20 | empty |
Compared structures
- 1ODN · Isopenicillin N synthase from aspergillus nidulans (oxygen-exposed product from anaerobic… · the same entry in another collection · chain A against A, TM-score 1.00
- P05326 · AlphaFold monomer V2.0 prediction for isopenicillin N synthase (P05326) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P05326
- Elsewhere: RCSB PDB 1ODN · PDBe 1ODN · UniProt P05326
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