Research workbench
Crystal structure of leubat (DELTA6 mutant) in complex with (S)- duloxetine
Analyse Crystal structure of leubat (DELTA6 mutant) in complex with (S)- duloxetine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MMD
- Type
- protein
- Length
- 1,008 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transporter
- UniProt
- O67854
- Ligands
- 29E, NA
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 80% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Transporter | protein | 504 | 80% helix, 1% strand | O67854 |
Ligands and binding sites
- 29E · (3S)-N-methyl-3-(naphthalen-1-yloxy)-3-(thiophen-2-yl) propan-1-amine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.82 | 0.96 | 22 | empty |
| 2 | 830 | 0.77 | 0.81 | 74 | 29E |
| 3 | 847 | 0.77 | 0.80 | 69 | 29E |
| 4 | 306 | 0.66 | 0.81 | 29 | empty |
| 5 | 115 | 0.59 | 0.85 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1404 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4MMD · Crystal structure of LeuBAT (delta6 mutant) in complex with (S)-duloxetine · the same entry in another collection · 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 O67854
- Elsewhere: RCSB PDB 4MMD · PDBe 4MMD · UniProt O67854
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