Research workbench
Structure of the M1 alanylaminopeptidase from malaria complexed with the phosphinate dipeptide analog
Analyse Structure of the M1 alanylaminopeptidase from malaria complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EBI
- Type
- protein
- Length
- 889 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- M1 family aminopeptidase
- EC
- 3.4.11.-
- UniProt
- O96935
- Ligands
- BEY, MG, ZN
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | M1 family aminopeptidase (EC 3.4.11.-) | protein | 889 | 45% helix, 22% strand | O96935 |
Ligands and binding sites
- BEY · (2S)-3-[(R)-[(1S)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]-2-benzylpropanoic acid · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.83 | 0.87 | 98 | BEY, GOL, MG |
| 2 | 231 | 0.69 | 0.85 | 33 | empty |
| 3 | 68 | 0.64 | 0.92 | 21 | empty |
| 4 | 59 | 0.61 | 0.92 | 16 | GOL |
| 5 | 424 | 0.61 | 0.76 | 56 | GOL |
Compared structures
- 3EBI · Structure of the M1 Alanylaminopeptidase from malaria complexed with the phosphinate… · the same entry in another collection · chain A against A, TM-score 1.00
- O96935 · AlphaFold monomer V2.0 prediction for M1 family aminopeptidase (O96935) · a predicted model of the same protein · 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 O96935
- Elsewhere: RCSB PDB 3EBI · PDBe 3EBI · UniProt O96935
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