Research workbench
Crystal structure of a proline dipeptidase from streptococcus pneumoniae TIGR4
Analyse Crystal structure of a proline dipeptidase from streptococcus pneumoniae TIGR4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PN9
- Type
- protein
- Length
- 544 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline dipeptidase
- EC
- 3.4.13.9
- UniProt
- Q97PL5
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline dipeptidase (EC 3.4.13.9) | protein | 138 | 40% helix, 19% strand | Q97PL5 |
| B, D | Proline dipeptidase (EC 3.4.13.9) | protein | 135 | 40% helix, 19% strand | Q97PL5 |
| C | Proline dipeptidase (EC 3.4.13.9) | protein | 136 | 40% helix, 19% strand | Q97PL5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 427 | 0.61 | 0.76 | 44 | SO4 |
| 2 | 218 | 0.51 | 0.76 | 25 | empty |
| 3 | 91 | 0.42 | 0.78 | 19 | empty |
| 4 | 78 | 0.35 | 0.76 | 13 | empty |
| 5 | 70 | 0.33 | 0.76 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–B · 626 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 357 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 355 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 39 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3PN9 · Crystal structure of a proline dipeptidase from streptococcus pneumoniae tigr4 · 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 Q97PL5
- Elsewhere: RCSB PDB 3PN9 · PDBe 3PN9 · UniProt Q97PL5
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