Research workbench
Crystal structure of the FK506-binding domain of plasmodium falciparum FKBP35 in complex with FK506
Analyse Crystal structure of the FK506-binding domain of plasmodium falciparum FKBP35… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VN1
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 70 kda peptidylprolyl isomerase
- EC
- 5.2.1.8
- UniProt
- Q8I4V8
- Ligands
- FK5
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 70 kda peptidylprolyl isomerase (EC 5.2.1.8) | protein | 123 | 13% helix, 39% strand | Q8I4V8 |
| B | 70 kda peptidylprolyl isomerase (EC 5.2.1.8) | protein | 123 | 11% helix, 38% strand | Q8I4V8 |
Ligands and binding sites
- FK5 · 8-deethyl-8-[but-3-enyl]-ascomycin · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.75 | 0.79 | 65 | FK5 |
| 2 | 73 | 0.38 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 437 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2VN1 · Crystal structure of the FK506-binding domain of Plasmodium falciparum FKBP35 in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8I4V8 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP35 (Q8I4V8) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8I4V8
- Elsewhere: RCSB PDB 2VN1 · PDBe 2VN1 · UniProt Q8I4V8
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