Research workbench
Structure of leucyl aminopeptidase from trypanosoma brucei in complex with actinonin
Analyse Structure of leucyl aminopeptidase from trypanosoma brucei 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
- 5NSQ
- Type
- protein
- Length
- 3,109 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase, putative
- UniProt
- Q385B0
- Ligands
- BB2, MN
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Aminopeptidase, putative | protein | 519 | 38% helix, 22% strand | Q385B0 |
| C | Aminopeptidase, putative | protein | 518 | 38% helix, 22% strand | Q385B0 |
| F | Aminopeptidase, putative | protein | 515 | 38% helix, 22% strand | Q385B0 |
Ligands and binding sites
- BB2 · Actinonin · ligand · 6 copies · chains A, B, C, D, F, E
- MN · Manganese (II) ion · metal · 12 copies · chains A, B, C, D, E, F
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 | 1128 | 0.72 | 0.76 | 108 | BB2 |
| 2 | 454 | 0.71 | 0.81 | 66 | empty |
| 3 | 225 | 0.69 | 0.86 | 41 | empty |
| 4 | 233 | 0.69 | 0.85 | 46 | empty |
| 5 | 497 | 0.68 | 0.79 | 65 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1680 Ų buried · 34 hydrogen bonds · protein-protein
- D–F · 1604 Ų buried · 33 hydrogen bonds · protein-protein
- A–E · 1595 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 1263 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1259 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5NSQ · Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Actinonin · 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 5NSQ · PDBe 5NSQ · UniProt Q385B0
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