Research workbench
Crystal structure of fkbp-frb T2098L mutant in complex with rapamycin
Analyse Crystal structure of fkbp-frb T2098L mutant in complex with rapamycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6M4U
- Type
- protein
- Length
- 406 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-prolyl cis-trans isomerase FKBP1A; SERINE/THREONINE-protein kinase mtor
- EC
- 5.2.1.8, 2.7.11.1
- UniProt
- P62942, P42345
- Ligands
- RAP, ZN, CL
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptidyl-prolyl cis-trans isomerase FKBP1A (EC 5.2.1.8) | protein | 108 | 12% helix, 40% strand | P62942 |
| B | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 93 | 87% helix, 0% strand | P42345 |
| E | Peptidyl-prolyl cis-trans isomerase FKBP1A (EC 5.2.1.8) | protein | 110 | 13% helix, 39% strand | P62942 |
| F | SERINE/THREONINE-protein kinase mtor (EC 2.7.11.1) | protein | 95 | 85% helix, 0% strand | P42345 |
Ligands and binding sites
- RAP · Rapamycin immunosuppressant drug · ligand · 2 copies · chains A, B, F, E
- ZN · Zinc ion · metal · 14 copies · chains A, B, F, E
- CL · Chloride ion · ion · 7 copies · chains A, E, B, F
- GOL · Glycerol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.83 | 0.83 | 63 | RAP, ZN |
| 2 | 641 | 0.80 | 0.85 | 46 | RAP |
| 3 | 105 | 0.53 | 0.83 | 17 | ZN, CL |
| 4 | 76 | 0.47 | 0.82 | 17 | ZN |
Interfaces
6 interfaces between chains.
- B–F · 553 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 395 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 326 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 210 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 178 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6M4U · Crystal structure of FKBP-FRB T2098L mutant in complex with rapamycin · the same entry in another collection · chain F against F, 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 0.98
- 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 0.97
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
- Every structure of UniProt P42345
- Elsewhere: RCSB PDB 6M4U · PDBe 6M4U · UniProt P62942 · UniProt P42345
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