MolNFT v1 · #120106 · protein
Co-crystal structure of the FK506 binding domain of human FKBP25, rapamycin and the frb domain of human mtor
5GPG · Peptidyl-prolyl cis-trans isomerase FKBP3: “Co-crystal structure of the FK506 binding domain of human FKBP25, rapamycin and the frb domain of human mtor”. X-ray diffraction, 1 ligand (RAP), 1 pocket (best druggability 0.78). MolNFT…
- PDB
- 5GPG
- Type
- protein
- Length
- 203 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase FKBP3; SERINE/THREONINE-protein kinase mtor
- EC
- 5.2.1.8, 2.7.11.1
- UniProt
- Q00688, P42345
- Ligands
- RAP
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase FKBP3 (EC 5.2.1.8) | protein | 110 | 14% helix, 38% strand | Q00688 |
| B | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 93 | 85% helix, 0% strand | P42345 |
Ligands and binding sites
- RAP · Rapamycin immunosuppressant drug · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.78 | 0.82 | 51 | RAP |
Interfaces
1 interface between chains.
- A–B · 529 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (artifact).
Compared structures
- 5GPG · Co-crystal structure of the FK506 binding domain of human FKBP25, Rapamycin and the FRB… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00688 · AlphaFold monomer V2.0 prediction for peptidyl-prolyl cis-trans isomerase FKBP3 (Q00688) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P42345 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase mtor (P42345) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q00688
- Every structure of UniProt P42345
- Elsewhere: RCSB PDB 5GPG · PDBe 5GPG · UniProt Q00688 · UniProt P42345
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