MolNFT v1 · #138266 · protein
A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis
5WDL · Aminopeptidase C: “A processive dipeptidyl aminopeptidase secreted from an established commensal bacterium P. distasonis”. X-ray diffraction, 2 ligands (R33, K), 14 pockets (best druggability 0.78). MolNFT v1 #138266 on GenesisL1…
- PDB
- 5WDL
- Type
- protein
- Length
- 2,226 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase C
- UniProt
- A6LE66
- Ligands
- R33, K
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase C | protein | 372 | 39% helix, 19% strand | A6LE66 |
| B | Aminopeptidase C | protein | 368 | 37% helix, 19% strand | A6LE66 |
| C | Aminopeptidase C | protein | 367 | 38% helix, 19% strand | A6LE66 |
| D, E, F | Aminopeptidase C | protein | 373 | 38% helix, 18% strand | A6LE66 |
Ligands and binding sites
- R33 · N-[(3S)-6-carbamimidamido-2-oxohexan-3-yl]glycinamide · ligand · 6 copies · chains A, B, C, D, E, F
- K · Potassium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.78 | 0.80 | 107 | R33 |
| 2 | 855 | 0.78 | 0.81 | 103 | R33 |
| 3 | 638 | 0.74 | 0.80 | 67 | empty |
| 4 | 261 | 0.66 | 0.83 | 56 | R33 |
| 5 | 232 | 0.65 | 0.83 | 54 | R33 |
Interfaces
9 interfaces between chains.
- A–F · 1503 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1499 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1490 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1181 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1163 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 5WDL · 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 5WDL · PDBe 5WDL · UniProt A6LE66
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