Research workbench
Crystal structure of FK506 binding domain of plasmodium falciparum FKBP35 in complex with D44
Analyse Crystal structure of FK506 binding domain of plasmodium falciparum FKBP35 in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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