Research workbench
X-ray crystallographic determination of the structure of bovine lens leucine aminopeptidase complexed with amastatin: formulation of a catalytic mechanism featuring a gem-diolate transition state
Analyse X-ray crystallographic determination of the structure of bovine lens leucine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BLL
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Leucine aminopeptidase; Amastatin
- EC
- 3.4.11.1
- UniProt
- P00727
- Ligands
- L2O, ZN
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Leucine aminopeptidase (EC 3.4.11.1) | protein | 481 | 39% helix, 21% strand | P00727 |
| I | Amastatin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- L2O · (2S,3R)-3-amino-2-hydroxy-5-methylhexanoic acid · ligand · chains E, I
- ZN · Zinc ion · metal · 2 copies · chains E, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.52 | 0.77 | 31 | L2O |
| 2 | 50 | 0.48 | 0.86 | 18 | empty |
| 3 | 134 | 0.42 | 0.75 | 21 | empty |
| 4 | 70 | 0.36 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- E–I · 275 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1BLL · X-ray crystallographic determination of the structure of bovine lens leucine… · the same entry in another collection · chain E against E, TM-score 1.00
- P00727 · AlphaFold monomer V2.0 prediction for cytosol aminopeptidase (P00727) · a predicted model of the same protein · chain E 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 P00727
- Elsewhere: RCSB PDB 1BLL · PDBe 1BLL · UniProt P00727
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