Research workbench
Candida albicans FKBP12 P104G protein bound with FK506 in C2 space group
Analyse Candida albicans FKBP12 P104G protein bound with FK506 in C2 space group in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HW8
- Type
- protein
- Length
- 932 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- FK506-binding protein 1
- EC
- 5.2.1.8
- UniProt
- P28870
- Ligands
- FK5
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 8 distinct chains · 10% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | FK506-binding protein 1 (EC 5.2.1.8) | protein | 120 | 12% helix, 35% strand | P28870 |
| B | FK506-binding protein 1 (EC 5.2.1.8) | protein | 122 | 11% helix, 34% strand | P28870 |
| C | FK506-binding protein 1 (EC 5.2.1.8) | protein | 121 | 12% helix, 38% strand | P28870 |
| D | FK506-binding protein 1 (EC 5.2.1.8) | protein | 120 | 8% helix, 35% strand | P28870 |
| E | FK506-binding protein 1 (EC 5.2.1.8) | protein | 118 | 8% helix, 36% strand | P28870 |
| F | FK506-binding protein 1 (EC 5.2.1.8) | protein | 110 | 10% helix, 30% strand | P28870 |
| G | FK506-binding protein 1 (EC 5.2.1.8) | protein | 121 | 8% helix, 38% strand | P28870 |
| H | FK506-binding protein 1 (EC 5.2.1.8) | protein | 100 | 8% helix, 38% strand | P28870 |
Ligands and binding sites
- FK5 · 8-deethyl-8-[but-3-enyl]-ascomycin · ligand · 8 copies · chains A, D, B, E, F, C, H, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.79 | 0.82 | 77 | FK5 |
| 2 | 756 | 0.78 | 0.82 | 81 | FK5 |
| 3 | 200 | 0.57 | 0.80 | 31 | empty |
| 4 | 310 | 0.54 | 0.74 | 38 | FK5 |
| 5 | 102 | 0.53 | 0.82 | 13 | FK5 |
Interfaces
15 interfaces between chains.
- A–B · 550 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 425 Ų buried · 4 hydrogen bonds · protein-protein
- E–G · 364 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 313 Ų buried · 4 hydrogen bonds · protein-protein
- B–F · 269 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5HW8 · Candida albicans FKBP12 P104G protein bound with FK506 in C2 space group · the same entry in another collection · chain H against H, TM-score 1.00
- P28870 · AlphaFold monomer V2.0 prediction for FK506-binding protein 1 (P28870) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 P28870
- Elsewhere: RCSB PDB 5HW8 · PDBe 5HW8 · UniProt P28870
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