MolNFT v1 · #128531 · protein
Structure of leucyl aminopeptidase from trypanosoma brucei in complex with bestatin
5NTD: “Structure of leucyl aminopeptidase from trypanosoma brucei in complex with bestatin”. X-ray diffraction, 4 ligands (BES, BCT, MN), 20 pockets (best druggability 0.70). MolNFT v1 #128531 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5NTD
- Type
- protein
- Length
- 6,228 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucyl aminopeptidase
- UniProt
- Q385B0
- Ligands
- BES, BCT, MN, SO4
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, H, I, J, K, L | Leucyl aminopeptidase | protein | 519 | 38% helix, 22% strand | Q385B0 |
| C | Leucyl aminopeptidase | protein | 518 | 38% helix, 22% strand | Q385B0 |
| G | Leucyl aminopeptidase | protein | 520 | 38% helix, 22% strand | Q385B0 |
Ligands and binding sites
- BES · 2-(3-amino-2-hydroxy-4-phenyl-butyrylamino)-4-methyl-pentanoic acid · ligand · 12 copies · chains A, B, D, C, E, F, G, H, I, J, K, L
- BCT · Bicarbonate ion · ligand · 12 copies · chains A, B, D, C, E, F, G, H, I, J, K, L
- MN · Manganese (II) ion · metal · 24 copies · chains A, B, D, C, E, F, G, H, I, J, K, L
- SO4 · Sulfate ion · ion · 11 copies · chains A, E, B, C, D, F, G, H, I, J, K, L
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 3 copies · chains A, C, L, E
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 | 220 | 0.70 | 0.87 | 37 | empty |
| 2 | 661 | 0.69 | 0.77 | 70 | BES, BCT |
| 3 | 215 | 0.68 | 0.86 | 40 | empty |
| 4 | 628 | 0.68 | 0.77 | 71 | BES, BCT |
| 5 | 626 | 0.68 | 0.77 | 58 | BES, BCT |
Interfaces
25 interfaces between chains.
- B–C · 1622 Ų buried · 37 hydrogen bonds · protein-protein
- D–F · 1586 Ų buried · 35 hydrogen bonds · protein-protein
- A–E · 1575 Ų buried · 36 hydrogen bonds · protein-protein
- J–K · 1281 Ų buried · 26 hydrogen bonds · protein-protein
- J–L · 1278 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5NTD · Structure of Leucyl aminopeptidase from Trypanosoma brucei in complex with Bestatin · 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 5NTD · PDBe 5NTD · UniProt Q385B0
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