MolNFT v1 · #182099 · protein
5-ht bound serotonin transporter reconstituted in lipid nanodisc in nacl in occluded conformation
7MGW · Sodium-dependent serotonin transporter: “5-ht bound serotonin transporter reconstituted in lipid nanodisc in nacl in occluded conformation”. Electron microscopy, 8 ligands (HP6, D12, SRO), 12 pockets (best druggability 0.73). MolNFT…
- PDB
- 7MGW
- 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, SRO, LNK, D10, CLR, NAG, CL
- Pockets
- 12 · best druggability 0.73
Structure
electron microscopy · 3 distinct chains · 48% helix, 13% 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, 39% strand | — |
| C | Variable domain of 15B8 antiboty Fab light chain | protein | 110 | 0% helix, 43% strand | — |
Ligands and binding sites
- HP6 · Heptane · ligand · 6 copies · chains A
- D12 · Dodecane · ligand · 4 copies · chains A
- SRO · Serotonin · ligand · 2 copies · chains A
- LNK · Pentane · ligand · chains A
- D10 · Decane · ligand · chains A
- CLR · Cholesterol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.73 | 0.97 | 15 | SRO |
| 2 | 337 | 0.70 | 0.83 | 47 | SRO |
| 3 | 379 | 0.62 | 0.78 | 33 | empty |
| 4 | 96 | 0.59 | 0.87 | 20 | empty |
| 5 | 84 | 0.52 | 0.84 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 921 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 291 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 disulfide, 1 glycan (covalent ligand, disulfide, N-glycosylation).
Compared structures
- 7MGW · 5-HT bound serotonin transporter reconstituted in lipid nanodisc in 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 0.95
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 7MGW · PDBe 7MGW · UniProt P31645
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