MolNFT v1 · #27250 · protein
Structure of plasmepsin II in complex of an pepstatin analogue
1XE5 · Plasmepsin 2: “Structure of plasmepsin II in complex of an pepstatin analogue”. X-ray diffraction, 1 ligand (5FE), 5 pockets (best druggability 0.82). MolNFT v1 #27250 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XE5
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plasmepsin 2
- EC
- 3.4.23.39
- UniProt
- P46925
- Ligands
- 5FE
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Plasmepsin 2 (EC 3.4.23.39) | protein | 329 | 14% helix, 46% strand | P46925 |
Ligands and binding sites
- 5FE · 5,5,5-trifluoro-3-hydroxy-4-[2-(5,5,5-trifluoro-3-hydroxy-4-{3-methyl-2-[3-methyl-2-(3-methyl-butyrylamino)-butyrylamino]-butyrylamino}-pentanoylamino)-propionylamino]-pentanoic acid methyl ester · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.82 | 0.83 | 97 | 5FE |
| 2 | 210 | 0.58 | 0.80 | 31 | empty |
| 3 | 132 | 0.45 | 0.77 | 26 | empty |
| 4 | 72 | 0.37 | 0.78 | 20 | empty |
| 5 | 54 | 0.26 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1297 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
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 P46925
- Elsewhere: RCSB PDB 1XE5 · PDBe 1XE5 · UniProt P46925
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