MolNFT v1 · #51581 · protein
Isopenicillin N synthase with substrate analogue L,L,L-acab (unexposed)
2VBP · Isopenicillin N synthetase: “Isopenicillin N synthase with substrate analogue L,L,L-acab (unexposed)”. X-ray diffraction, 3 ligands (VB1, FE2, SO4), 1 pocket (best druggability 0.81). MolNFT v1 #51581 on GenesisL1: 3D structure…
- PDB
- 2VBP
- Type
- protein
- Length
- 329 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isopenicillin N synthetase
- EC
- 1.21.3.1
- UniProt
- P05326
- Ligands
- VB1, FE2, SO4
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isopenicillin N synthetase (EC 1.21.3.1) | protein | 329 | 30% helix, 22% strand | P05326 |
Ligands and binding sites
- VB1 · N^6^-[(1R)-2-{[(1S)-1-carboxypropyl]amino}-2-oxo-1-(sulfanylmethyl)ethyl]-6-oxo-L-lysine · ligand · chains A
- FE2 · Fe (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 522 | 0.81 | 0.87 | 65 | FE2, VB1 |
Compared structures
- 2VBP · Isopenicillin N synthase with substrate analogue L,L,L-ACAB (unexposed) · 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 2VBP · PDBe 2VBP · UniProt P05326
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