Research workbench
Unliganded structure of leucyl aminopeptidase from trypanosoma brucei
Analyse Unliganded structure of leucyl aminopeptidase from trypanosoma brucei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NSM
- Type
- protein
- Length
- 6,228 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase, putative
- UniProt
- Q385B0
- Ligands
- BCT, MN
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Aminopeptidase, putative | protein | 519 | 38% helix, 22% strand | Q385B0 |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MN · Manganese (II) ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.75 | 0.78 | 106 | BCT |
| 2 | 217 | 0.70 | 0.86 | 39 | empty |
| 3 | 613 | 0.69 | 0.78 | 61 | BCT |
| 4 | 650 | 0.69 | 0.77 | 61 | BCT |
| 5 | 401 | 0.68 | 0.81 | 55 | empty |
Interfaces
23 interfaces between chains.
- C–H · 1601 Ų buried · 39 hydrogen bonds · protein-protein
- E–G · 1596 Ų buried · 38 hydrogen bonds · protein-protein
- F–I · 1583 Ų buried · 37 hydrogen bonds · protein-protein
- C–F · 1307 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1302 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5NSM · unliganded Structure of Leucyl aminopeptidase from Trypanosoma brucei · 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 Q385B0
- Elsewhere: RCSB PDB 5NSM · PDBe 5NSM · UniProt Q385B0
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