MolNFT v1 · #75968 · protein
Xaa-pro dipeptidase from bacillus anthracis.
3Q6D · Proline dipeptidase: “Xaa-pro dipeptidase from bacillus anthracis.”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.73). MolNFT v1 #75968 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3Q6D
- Type
- protein
- Length
- 1,416 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline dipeptidase
- EC
- 3.4.13.9
- UniProt
- Q81M33
- Ligands
- CA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proline dipeptidase (EC 3.4.13.9) | protein | 355 | 38% helix, 25% strand | Q81M33 |
| C | Proline dipeptidase (EC 3.4.13.9) | protein | 353 | 39% helix, 25% strand | Q81M33 |
| D | Proline dipeptidase (EC 3.4.13.9) | protein | 353 | 39% helix, 24% strand | Q81M33 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.73 | 0.83 | 49 | GOL |
| 2 | 485 | 0.65 | 0.77 | 69 | empty |
| 3 | 216 | 0.55 | 0.78 | 20 | empty |
| 4 | 189 | 0.51 | 0.77 | 24 | CA |
| 5 | 114 | 0.47 | 0.79 | 16 | empty |
Interfaces
4 interfaces between chains.
- C–D · 863 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 855 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 385 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 328 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3Q6D · Xaa-Pro dipeptidase from Bacillus anthracis. · 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 Q81M33
- Elsewhere: RCSB PDB 3Q6D · PDBe 3Q6D · UniProt Q81M33
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