Research workbench
Structure of slyd delta-if from thermus thermophilus in complex with FK506
Analyse Structure of slyd delta-if from thermus thermophilus in complex with FK506 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ODR
- Type
- protein
- Length
- 209 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase slyd, peptidyl-prolyl cis-trans isomerase FKBP1A…
- EC
- 5.2.1.8
- UniProt
- Q5SLE7, P62942
- Ligands
- FK5, ZN, CL
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase slyd, peptidyl-prolyl cis-trans isomerase FKBP1A chimera (EC 5.2.1.8) | protein | 104 | 15% helix, 42% strand | Q5SLE7, P62942 |
| B | Peptidyl-prolyl cis-trans isomerase slyd, peptidyl-prolyl cis-trans isomerase FKBP1A chimera (EC 5.2.1.8) | protein | 105 | 15% helix, 42% strand | Q5SLE7, P62942 |
Ligands and binding sites
- FK5 · 8-deethyl-8-[but-3-enyl]-ascomycin · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
- ACT · Acetate ion · additive · 3 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 | 231 | 0.54 | 0.77 | 28 | GOL, FK5 |
| 2 | 188 | 0.49 | 0.75 | 28 | FK5 |
Interfaces
1 interface between chains.
- A–B · 582 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4ODR · Structure of SlyD delta-IF from Thermus thermophilus in complex with FK506 · the same entry in another collection · chain A against A, TM-score 1.00
- P62942 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP1A (P62942) · a predicted model of the same protein · chain A against A, TM-score 0.80
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 Q5SLE7
- Every structure of UniProt P62942
- Elsewhere: RCSB PDB 4ODR · PDBe 4ODR · UniProt Q5SLE7 · UniProt P62942
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