MolNFT v1 · #123659 · protein
The xray crystal structure of P. falciparum aminopeptidase P in complex with apstatin
5JR6 · Peptidase, putative: “The xray crystal structure of P. falciparum aminopeptidase P in complex with apstatin”. X-ray diffraction, 4 ligands (01B, MN, NH2), 13 pockets (best druggability 0.78). MolNFT v1 #123659 on GenesisL1: 3D…
- PDB
- 5JR6
- Type
- protein
- Length
- 1,176 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase, putative; Apstatin
- UniProt
- Q8IKT5
- Ligands
- 01B, MN, NH2, PO4
- Pockets
- 13 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidase, putative | protein | 628 | 38% helix, 23% strand | Q8IKT5 |
| B | Peptidase, putative | protein | 545 | 37% helix, 23% strand | Q8IKT5 |
| F | Apstatin | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 01B · (2S,3R)-3-amino-2-hydroxy-4-phenylbutanoic acid · ligand · chains A, F
- MN · Manganese (II) ion · metal · 4 copies · chains A, F, B
- NH2 · Amino group · ion · chains A, F
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.78 | 0.80 | 109 | 01B, NH2 |
| 2 | 930 | 0.72 | 0.76 | 97 | PO4 |
| 3 | 104 | 0.61 | 0.87 | 19 | empty |
| 4 | 406 | 0.60 | 0.76 | 34 | empty |
| 5 | 294 | 0.60 | 0.78 | 39 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1209 Ų buried · 16 hydrogen bonds · protein-protein
- A–F · 261 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5JR6 · The Xray Crystal Structure of P. falciparum Aminopeptidase P in Complex With Apstatin · 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 Q8IKT5
- Elsewhere: RCSB PDB 5JR6 · PDBe 5JR6 · UniProt Q8IKT5
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