Research workbench
Crystal structure of 11BETA-HSD1 double mutant (L262R, F278E) complexed with 2-(2-benzyl-6-hydroxyadamantan-2-yl)-1-(3- hydroxyazetidin-1-YL)ETHAN-1-one
Analyse Crystal structure of 11BETA-HSD1 double mutant (L262R, F278E) complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5PGX
- Type
- protein
- Length
- 1,079 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Corticosteroid 11-beta-dehydrogenase isozyme 1
- EC
- 1.1.1.146
- UniProt
- P28845
- Ligands
- NAP, 8KD
- Pockets
- 13 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 262 | 52% helix, 14% strand | P28845 |
| B | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 280 | 49% helix, 13% strand | P28845 |
| D | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 274 | 50% helix, 14% strand | P28845 |
| E | Corticosteroid 11-beta-dehydrogenase isozyme 1 (EC 1.1.1.146) | protein | 263 | 52% helix, 14% strand | P28845 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, D, E
- 8KD · 2-(2-benzyl-6-hydroxyadamantan-2-yl)-1-(3-hydroxyazetidin-1-yl)ethan-1-one · ligand · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.84 | 0.87 | 71 | NAP, 8KD |
| 2 | 646 | 0.84 | 0.88 | 65 | NAP, 8KD |
| 3 | 772 | 0.83 | 0.86 | 75 | NAP, 8KD |
| 4 | 790 | 0.82 | 0.85 | 73 | NAP, 8KD |
| 5 | 786 | 0.78 | 0.81 | 106 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2754 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 2613 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 420 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 360 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 109 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5PGX · Crystal structure of 11BETA-HSD1 double mutant (L262R, F278E) complexed with… · the same entry in another collection · chain E against E, TM-score 1.00
- P28845 · AlphaFold monomer V2.0 prediction for corticosteroid 11-beta- dehydrogenase isozyme 1… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P28845
- Elsewhere: RCSB PDB 5PGX · PDBe 5PGX · UniProt P28845
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