MolNFT v1 · #7879 · protein
Structure-based prediction of modifications in glutarylamidase to allow single-step enzymatic production of 7-aminocephalosporanic acid from cephalosporin C
1GK0 · Cephalosporin acylase: “Structure-based prediction of modifications in glutarylamidase to allow single-step enzymatic production of…”. X-ray diffraction, 1 ligand (PO4), 11 pockets (best druggability 0.61). MolNFT v1 #7879 on…
- PDB
- 1GK0
- Type
- protein
- Length
- 1,350 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cephalosporin acylase
- EC
- 3.5.1.11
- UniProt
- O86089
- Ligands
- PO4
- Pockets
- 11 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cephalosporin acylase (EC 3.5.1.11) | protein | 153 | 69% helix, 5% strand | O86089 |
| B, D | Cephalosporin acylase (EC 3.5.1.11) | protein | 522 | 25% helix, 29% strand | O86089 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains B, D
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.61 | 0.77 | 63 | PO4, EDO |
| 2 | 369 | 0.59 | 0.76 | 63 | PO4, EDO |
| 3 | 144 | 0.49 | 0.78 | 23 | empty |
| 4 | 112 | 0.46 | 0.79 | 20 | empty |
| 5 | 166 | 0.41 | 0.73 | 28 | empty |
Interfaces
4 interfaces between chains.
- C–D · 4110 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 4089 Ų buried · 55 hydrogen bonds · protein-protein
- B–D · 229 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 211 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1GK0 · Structure-based prediction of modifications in glutarylamidase to allow single-step… · the same entry in another collection · chain C against C, TM-score 1.00
- 1GK1 · Structure-based prediction of modifications in glutarylamidase to allow single-step… · an experimental structure of the same protein · chain B against B, 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 O86089
- Elsewhere: RCSB PDB 1GK0 · PDBe 1GK0 · UniProt O86089 · AlphaFold DB O86089
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