MolNFT v1 · #181030 · protein
5-ht bound serotonin transporter reconstituted in lipid nanodisc in presence of nacl in outward facing conformation
7LIA · Sodium-dependent serotonin transporter: “5-ht bound serotonin transporter reconstituted in lipid nanodisc in presence of nacl in outward facing…”. Electron microscopy, 8 ligands (HP6, D10, SRO), 7 pockets (best druggability 0.77).…
- PDB
- 7LIA
- Type
- protein
- Length
- 767 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, D10, SRO, LNK, CLR, NAG, NA, CL
- Pockets
- 7 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 539 | 69% helix, 1% strand | P31645 |
| B | Variable domain of 15B8 antibody Fab heavy chain | protein | 118 | 8% helix, 46% strand | — |
| C | Variable domain of 15B8 antibody Fab light chain | protein | 110 | 0% helix, 48% strand | — |
Ligands and binding sites
- HP6 · Heptane · ligand · 13 copies · chains A
- D10 · Decane · ligand · 5 copies · chains A
- SRO · Serotonin · ligand · 2 copies · chains A
- LNK · Pentane · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.77 | 0.95 | 25 | SRO |
| 2 | 449 | 0.69 | 0.80 | 44 | SRO |
| 3 | 467 | 0.66 | 0.78 | 54 | empty |
| 4 | 80 | 0.38 | 0.76 | 16 | HP6 |
| 5 | 81 | 0.35 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 844 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 462 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 258 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7LIA · 5-HT bound serotonin transporter reconstituted in lipid nanodisc in presence of NaCl in… · 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 0.98
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 P31645
- Elsewhere: RCSB PDB 7LIA · PDBe 7LIA · UniProt P31645
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