Research workbench
Trypanosoma cruzi proline racemase in complex with inhibitor NG-P27
Analyse Trypanosoma cruzi proline racemase in complex with inhibitor NG-P27 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HJE
- Type
- protein
- Length
- 713 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Trypanosoma cruzi (strain CL Brener)
- Molecule
- Proline racemase A
- EC
- 5.1.1.4
- UniProt
- Q4DA80
- Ligands
- 7N0, PO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · resolution 2 · 2 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline racemase A (EC 5.1.1.4) | protein | 357 | 19% helix, 38% strand | Q4DA80 |
| B | Proline racemase A (EC 5.1.1.4) | protein | 356 | 20% helix, 40% strand | Q4DA80 |
Ligands and binding sites
- 7N0 · 2-[(1~{S})-2-oxidanylidenecyclopentyl]ethanoic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 604 | 0.75 | 0.82 | 36 | empty |
| 2 | 188 | 0.60 | 0.82 | 34 | 7N0 |
| 3 | 79 | 0.50 | 0.84 | 18 | empty |
| 4 | 52 | 0.43 | 0.83 | 17 | empty |
| 5 | 65 | 0.37 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1681 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
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 Q4DA80
- Elsewhere: RCSB PDB 6HJE · PDBe 6HJE · UniProt Q4DA80
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