Research workbench
Apo serotonin transporter reconstituted in lipid nanodisc in presence of nacl in occluded conformation
Analyse Apo serotonin transporter reconstituted in lipid nanodisc in presence of nacl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LI7
- Type
- protein
- Length
- 765 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-dependent serotonin transporter; Variable domain of 15B8 antibody Fab heavy chain…
- UniProt
- P31645
- Ligands
- HP6, D12, LNK, CLR, D10, NAG
- Pockets
- 12 · best druggability 0.70
Structure
electron microscopy · 3 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 537 | 69% helix, 1% strand | P31645 |
| B | Variable domain of 15B8 antibody Fab heavy chain | protein | 118 | 0% helix, 36% strand | — |
| C | Variable domain of 15B8 antibody Fab light chain | protein | 110 | 0% helix, 44% strand | — |
Ligands and binding sites
- HP6 · Heptane · ligand · 5 copies · chains A
- D12 · Dodecane · ligand · 3 copies · chains A
- LNK · Pentane · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- D10 · Decane · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.70 | 0.97 | 15 | empty |
| 2 | 273 | 0.61 | 0.80 | 35 | empty |
| 3 | 309 | 0.61 | 0.79 | 33 | empty |
| 4 | 127 | 0.55 | 0.83 | 19 | empty |
| 5 | 119 | 0.52 | 0.81 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 870 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 618 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 293 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 7LI7 · apo serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in occluded… · the same entry in another collection · chain A against A, TM-score 1.00
- P31645 · AlphaFold monomer V2.0 prediction for sodium-dependent serotonin transporter (P31645) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P31645
- Elsewhere: RCSB PDB 7LI7 · PDBe 7LI7 · UniProt P31645
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