MolNFT v1 · #138265 · protein
A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis
5WDK · Aminopeptidase C: “A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis”. X-ray diffraction, 2 ligands (T1O, K), 16 pockets (best druggability 0.79). MolNFT v1 #138265 on GenesisL1…
- PDB
- 5WDK
- Type
- protein
- Length
- 2,146 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase C
- UniProt
- A6LE66
- Ligands
- T1O, K
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase C | protein | 363 | 36% helix, 19% strand | A6LE66 |
| B | Aminopeptidase C | protein | 345 | 39% helix, 20% strand | A6LE66 |
| C | Aminopeptidase C | protein | 352 | 36% helix, 20% strand | A6LE66 |
| D | Aminopeptidase C | protein | 363 | 39% helix, 20% strand | A6LE66 |
| E | Aminopeptidase C | protein | 349 | 38% helix, 19% strand | A6LE66 |
| F | Aminopeptidase C | protein | 374 | 39% helix, 18% strand | A6LE66 |
Ligands and binding sites
- T1O · 5-[(3aS,4R,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(2-oxopropyl)pentanamide · ligand · 6 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 11 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.79 | 0.81 | 115 | T1O |
| 2 | 754 | 0.75 | 0.80 | 87 | empty |
| 3 | 700 | 0.72 | 0.79 | 78 | empty |
| 4 | 281 | 0.66 | 0.82 | 54 | empty |
| 5 | 185 | 0.60 | 0.82 | 38 | empty |
Interfaces
7 interfaces between chains.
- D–E · 1479 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 1466 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1457 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1174 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 1171 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5WDK · A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium… · 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 A6LE66
- Elsewhere: RCSB PDB 5WDK · PDBe 5WDK · UniProt A6LE66
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