MolNFT v1 · #81971 · protein
Crystal structure of an asymmetric trimer of a glutamate transporter homologue (gltph)
3V8G · Sodium-coupled L-aspartate transporter: “Crystal structure of an asymmetric trimer of a glutamate transporter homologue (gltph)”. X-ray diffraction, 2 ligands (ASP, NA), 20 pockets (best druggability 0.87). MolNFT v1 #81971 on…
- PDB
- 3V8G
- Type
- protein
- Length
- 2,421 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium-coupled L-aspartate transporter
- UniProt
- O59010
- Ligands
- ASP, NA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Sodium-coupled L-aspartate transporter | protein | 411 | 73% helix, 0% strand | O59010 |
| B | Sodium-coupled L-aspartate transporter | protein | 404 | 74% helix, 0% strand | O59010 |
| C | Sodium-coupled L-aspartate transporter | protein | 400 | 73% helix, 0% strand | O59010 |
| E | Sodium-coupled L-aspartate transporter | protein | 403 | 74% helix, 0% strand | O59010 |
| F | Sodium-coupled L-aspartate transporter | protein | 392 | 74% helix, 0% strand | O59010 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.87 | 0.90 | 59 | empty |
| 2 | 710 | 0.86 | 0.89 | 64 | empty |
| 3 | 1195 | 0.82 | 0.83 | 116 | empty |
| 4 | 736 | 0.68 | 0.75 | 65 | empty |
| 5 | 430 | 0.66 | 0.79 | 56 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1141 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 1112 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1111 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1096 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1077 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3V8G · Crystal structure of an asymmetric trimer of a glutamate transporter homologue (GltPh) · the same entry in another collection · chain F against F, TM-score 1.00
- O59010 · AlphaFold monomer V2.0 prediction for glutamate transporter homolog (O59010) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 O59010
- Elsewhere: RCSB PDB 3V8G · PDBe 3V8G · UniProt O59010
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