MolNFT v1 · #156459 · protein
Crystal structure of mbp fused split fkbp-frb T2098L mutant in complex with rapamycin
6M4W · Chimera of MALTOSE/MALTODEXTRIN-binding periplasmic protein…: “Crystal structure of mbp fused split fkbp-frb T2098L mutant in complex with rapamycin”. X-ray diffraction, 2 ligands (RAP, GLC), 19 pockets (best druggability 0.85).…
- PDB
- 6M4W
- Type
- protein
- Length
- 1,707 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of MALTOSE/MALTODEXTRIN-binding periplasmic protein and peptidyl-prolyl cis-trans…
- EC
- 5.2.1.8, 2.7.11.1
- UniProt
- P0AEX9, P62942, P42345
- Ligands
- RAP, GLC
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimera of MALTOSE/MALTODEXTRIN-binding periplasmic protein and peptidyl-prolyl cis-trans isomerase FKBP1A (EC 5.2.1.8) | protein | 403 | 39% helix, 22% strand | P0AEX9, P62942 |
| B | Chimera of MALTOSE/MALTODEXTRIN-binding periplasmic protein and peptidyl-prolyl cis-trans isomerase FKBP1A (EC 5.2.1.8) | protein | 399 | 40% helix, 22% strand | P0AEX9, P62942 |
| C | Chimera of MALTOSE/MALTODEXTRIN-binding periplasmic protein and peptidyl-prolyl cis-trans isomerase FKBP1A (EC 5.2.1.8) | protein | 399 | 41% helix, 22% strand | P0AEX9, P62942 |
| D | Peptidyl-prolyl cis-trans isomerase FKBP1A (EC 5.2.1.8) | protein | 75 | 12% helix, 35% strand | P62942 |
| E, F | Peptidyl-prolyl cis-trans isomerase FKBP1A (EC 5.2.1.8) | protein | 76 | 11% helix, 36% strand | P62942 |
| G, H, I | 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 · 3 copies · chains A, C, D, G, B, E, H, F, I
- GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A, B, C
- GOL · Glycerol · additive · chains G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.85 | 0.86 | 79 | RAP |
| 2 | 987 | 0.82 | 0.83 | 65 | RAP |
| 3 | 967 | 0.82 | 0.83 | 67 | RAP |
| 4 | 1114 | 0.81 | 0.82 | 87 | GLC |
| 5 | 534 | 0.80 | 0.86 | 49 | GLC |
Interfaces
20 interfaces between chains.
- B–E · 2201 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 2200 Ų buried · 46 hydrogen bonds · protein-protein
- C–F · 2177 Ų buried · 45 hydrogen bonds · protein-protein
- D–G · 480 Ų buried · 5 hydrogen bonds · protein-protein
- E–H · 472 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6M4W · Crystal structure of MBP fused split FKBP-FRB T2098L mutant in complex with rapamycin · the same entry in another collection · chain I against I, 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 D 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 G 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 P0AEX9
- Every structure of UniProt P62942
- Every structure of UniProt P42345
- Elsewhere: RCSB PDB 6M4W · PDBe 6M4W · UniProt P0AEX9 · UniProt P62942 · UniProt P42345
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