MolNFT v1 · #121458 · protein
Candida albicans FKBP12 P104G protein bound with FK506 in C2 space group
5HW8 · FK506-binding protein 1: “Candida albicans FKBP12 P104G protein bound with FK506 in C2 space group”. X-ray diffraction, 1 ligand (FK5), 12 pockets (best druggability 0.79). MolNFT v1 #121458 on GenesisL1: 3D structure, binding sites…
- 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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