MolNFT v1 · #181026 · protein
Apo sert reconstituted in lipid nanodisc in kcl
7LI6 · Sodium-dependent serotonin transporter: “Apo sert reconstituted in lipid nanodisc in kcl”. Electron microscopy, 7 ligands (HP6, D10, LNK), 13 pockets (best druggability 0.78). MolNFT v1 #181026 on GenesisL1: 3D structure, binding…
- PDB
- 7LI6
- 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, LNK, D12, R16, NAG, CL
- Pockets
- 13 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 44% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium-dependent serotonin transporter | protein | 539 | 62% helix, 1% strand | P31645 |
| B | Variable domain of 15B8 antibody Fab heavy chain | protein | 118 | 3% helix, 38% strand | — |
| C | Variable domain of 15B8 antibody Fab light chain | protein | 110 | 0% helix, 30% strand | — |
Ligands and binding sites
- HP6 · Heptane · ligand · 9 copies · chains A
- D10 · Decane · ligand · 6 copies · chains A
- LNK · Pentane · ligand · 4 copies · chains A
- D12 · Dodecane · ligand · 3 copies · chains A
- R16 · Hexadecane · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 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
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.78 | 0.83 | 61 | empty |
| 2 | 296 | 0.57 | 0.77 | 31 | empty |
| 3 | 243 | 0.55 | 0.78 | 36 | empty |
| 4 | 192 | 0.49 | 0.76 | 33 | empty |
| 5 | 74 | 0.41 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–C · 924 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 520 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 258 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
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 7LI6 · PDBe 7LI6 · UniProt P31645
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