Research workbench
Fkbp complexed with methyl methylsulfinylmethyl sulfide (dss)
Analyse Fkbp complexed with methyl methylsulfinylmethyl sulfide (dss) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D7I
- Type
- protein
- Length
- 214 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (FK506-binding protein)
- EC
- 5.2.1.8
- UniProt
- P62942
- Ligands
- DSS, NH4, SO4
- Pockets
- 1 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (FK506-binding protein) (EC 5.2.1.8) | protein | 107 | 11% helix, 40% strand | P62942 |
Ligands and binding sites
- DSS · Methyl methylsulfinylmethyl sulfide · ligand · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.36 | 0.77 | 13 | DSS |
Interfaces
1 interface between chains.
- A–B · 63 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1D7I · Fkbp complexed with methyl methylsulfinylmethyl sulfide (dss) · 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 0.99
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 P62942
- Elsewhere: RCSB PDB 1D7I · PDBe 1D7I · UniProt P62942
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