MolNFT v1 · #95917 · protein
Crystal structure of FK506 binding domain of plasmodium falciparum FKBP35 in complex with D44
4J4N · FK506-binding protein (fkbp)-type peptidyl-propyl isomerase: “Crystal structure of FK506 binding domain of plasmodium falciparum FKBP35 in complex with D44”. X-ray diffraction, 1 ligand (D44), 5 pockets (best druggability 0.78).…
- PDB
- 4J4N
- Type
- protein
- Length
- 366 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FK506-binding protein (fkbp)-type peptidyl-propyl isomerase
- EC
- 5.2.1.8
- UniProt
- Q8I4V8
- Ligands
- D44
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FK506-binding protein (fkbp)-type peptidyl-propyl isomerase (EC 5.2.1.8) | protein | 123 | 11% helix, 39% strand | Q8I4V8 |
| B | FK506-binding protein (fkbp)-type peptidyl-propyl isomerase (EC 5.2.1.8) | protein | 122 | 11% helix, 39% strand | Q8I4V8 |
| C | FK506-binding protein (fkbp)-type peptidyl-propyl isomerase (EC 5.2.1.8) | protein | 121 | 17% helix, 37% strand | Q8I4V8 |
Ligands and binding sites
- D44 · N-(2-ethylphenyl)-2-(3H-imidazo[4,5-b]pyridin-2-ylsulfanyl)acetamide · ligand · 3 copies · chains A, B, C
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 | 964 | 0.78 | 0.80 | 77 | D44 |
| 2 | 162 | 0.57 | 0.81 | 28 | empty |
| 3 | 60 | 0.35 | 0.77 | 13 | D44 |
| 4 | 61 | 0.32 | 0.76 | 14 | empty |
| 5 | 50 | 0.27 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 640 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 426 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 273 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4J4N · Crystal structure of FK506 binding domain of plasmodium falciparum FKBP35 in complex with… · 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 C against A, TM-score 0.99
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 4J4N · PDBe 4J4N · UniProt Q8I4V8
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