MolNFT v1 · #171938 · protein
The structure of glutamate transporter homologue glttk in complex with the photo switchable compound (trans)
6ZLH · PROTON/GLUTAMATE symporter, sdf family: “The structure of glutamate transporter homologue glttk in complex with the photo switchable compound (trans)”. X-ray diffraction, 2 ligands (QM5, NA), 17 pockets (best druggability 0.88).…
- PDB
- 6ZLH
- Type
- protein
- Length
- 1,270 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PROTON/GLUTAMATE symporter, sdf family
- UniProt
- Q5JID0
- Ligands
- QM5, NA
- Pockets
- 17 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PROTON/GLUTAMATE symporter, sdf family | protein | 424 | 77% helix, 0% strand | Q5JID0 |
| B, C | PROTON/GLUTAMATE symporter, sdf family | protein | 423 | 78% helix, 0% strand | Q5JID0 |
Ligands and binding sites
- QM5 · (2~{S},3~{S})-2-azanyl-3-[[4-[2-(4-methoxyphenyl) hydrazinyl]phenyl]methoxy]butanedioic acid · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 9 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 14 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 6 copies · chains A, B, C
- DMU · Decyl-beta-D-maltopyranoside · additive · 3 copies · chains A, C, B
- PG4 · Tetraethylene glycol · additive · 3 copies · chains A
- 1PE · Pentaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.88 | 0.92 | 46 | PEG |
| 2 | 388 | 0.59 | 0.76 | 43 | QM5, NA |
| 3 | 339 | 0.59 | 0.77 | 40 | QM5, NA |
| 4 | 340 | 0.58 | 0.76 | 49 | QM5, NA |
| 5 | 324 | 0.55 | 0.74 | 39 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1195 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1184 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1174 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6ZLH · the structure of glutamate transporter homologue GltTk in complex with the photo… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5JID0
- Elsewhere: RCSB PDB 6ZLH · PDBe 6ZLH · UniProt Q5JID0
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