Research workbench
Isopenicillin N synthase with the dipeptide substrate analogue ahc
Analyse Isopenicillin N synthase with the dipeptide substrate analogue ahc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BB3
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopenicillin N synthase
- EC
- 1.21.3.1
- UniProt
- P05326
- Ligands
- KKA, FE, SO4
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopenicillin N synthase (EC 1.21.3.1) | protein | 329 | 30% helix, 21% strand | P05326 |
Ligands and binding sites
- KKA · (2S)-2-azanyl-6-oxidanylidene-6-[[(2S)-1-oxidanyl-1-oxidanylidene-4-sulfanyl-butan-2-yl]amino]hexanoic acid · ligand · chains A
- FE · Fe (III) 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.82 | 0.88 | 59 | KKA |
| 2 | 50 | 0.29 | 0.76 | 16 | empty |
| 3 | 55 | 0.27 | 0.73 | 12 | empty |
Compared structures
- 4BB3 · Isopenicillin N synthase with the dipeptide substrate analogue AhC · 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 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 P05326
- Elsewhere: RCSB PDB 4BB3 · PDBe 4BB3 · UniProt P05326
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