MolNFT v1 · #115099 · protein
Structure of N-acylhomoserine lactone acylase macq shortened spacer mutant (DELTA202-208) in uncleaved form
5C9I · Protein related to penicillin acylase: “Structure of N-acylhomoserine lactone acylase macq shortened spacer mutant (DELTA202-208) in uncleaved form”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #115099 on…
- PDB
- 5C9I
- Type
- protein
- Length
- 3,027 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein related to penicillin acylase
- UniProt
- A0A0A1VBK6
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein related to penicillin acylase | protein | 768 | 33% helix, 24% strand | A0A0A1VBK6 |
| B | Protein related to penicillin acylase | protein | 762 | 35% helix, 25% strand | A0A0A1VBK6 |
| C | Protein related to penicillin acylase | protein | 751 | 34% helix, 25% strand | A0A0A1VBK6 |
| D | Protein related to penicillin acylase | protein | 746 | 34% helix, 25% strand | A0A0A1VBK6 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.81 | 0.83 | 106 | empty |
| 2 | 792 | 0.77 | 0.81 | 90 | empty |
| 3 | 259 | 0.76 | 0.89 | 46 | empty |
| 4 | 68 | 0.76 | 0.99 | 22 | empty |
| 5 | 60 | 0.75 | 0.99 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2206 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1007 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 868 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5C9I · Structure of N-acylhomoserine lactone acylase MacQ shortened spacer mutant (delta202-208)… · the same entry in another collection · 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 A0A0A1VBK6
- Elsewhere: RCSB PDB 5C9I · PDBe 5C9I · UniProt A0A0A1VBK6
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