Research workbench
Structure of slyd from thermus thermophilus in complex with FK506
Analyse Structure of slyd 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
- 4ODO
- Type
- protein
- Length
- 458 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase slyd
- EC
- 5.2.1.8
- UniProt
- Q5SLE7
- Ligands
- FK5, MG, CL
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase slyd (EC 5.2.1.8) | protein | 150 | 15% helix, 42% strand | Q5SLE7 |
| B | Peptidyl-prolyl cis-trans isomerase slyd (EC 5.2.1.8) | protein | 155 | 14% helix, 43% strand | Q5SLE7 |
| C | Peptidyl-prolyl cis-trans isomerase slyd (EC 5.2.1.8) | protein | 153 | 14% helix, 44% strand | Q5SLE7 |
Ligands and binding sites
- FK5 · 8-deethyl-8-[but-3-enyl]-ascomycin · ligand · 3 copies · chains A, C, B
- MG · Magnesium ion · metal · 4 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains B, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.73 | 0.78 | 73 | CL, FK5 |
| 2 | 1145 | 0.73 | 0.76 | 75 | CL, BTB, FK5, GOL |
| 3 | 257 | 0.66 | 0.83 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–B · 884 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 595 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 498 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4ODO · Structure of SlyD from Thermus thermophilus in complex with FK506 · 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 Q5SLE7
- Elsewhere: RCSB PDB 4ODO · PDBe 4ODO · UniProt Q5SLE7
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