Research workbench
Structure of leucyl aminopeptidase from trypanosoma cruzi in complex with citrate
Analyse Structure of leucyl aminopeptidase from trypanosoma cruzi in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NTG
- Type
- protein
- Length
- 1,022 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase
- UniProt
- V5BWE3
- Ligands
- MN, SO4
- Pockets
- 10 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminopeptidase | protein | 512 | 38% helix, 22% strand | V5BWE3 |
| B | Aminopeptidase | protein | 510 | 38% helix, 22% strand | V5BWE3 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CIT · Citric acid · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.63 | 0.79 | 48 | empty |
| 2 | 368 | 0.63 | 0.78 | 34 | CIT, SO4 |
| 3 | 189 | 0.62 | 0.83 | 34 | empty |
| 4 | 210 | 0.61 | 0.81 | 24 | CIT |
| 5 | 323 | 0.59 | 0.77 | 32 | CIT, SO4 |
Interfaces
1 interface between chains.
- A–B · 1517 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5NTG · Structure of Leucyl aminopeptidase from Trypanosoma cruzi in complex with citrate · 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 V5BWE3
- Elsewhere: RCSB PDB 5NTG · PDBe 5NTG · UniProt V5BWE3
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