Research workbench
The structure of glutamate transporter homologue glttk in complex with the photo switchable compound (cis)
Analyse The structure of glutamate transporter homologue glttk in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZL4
- 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
- 16 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 78% 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
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 569 | 0.87 | 0.92 | 49 | PEG |
| 2 | 396 | 0.61 | 0.77 | 44 | QM5 |
| 3 | 346 | 0.59 | 0.76 | 41 | QM5, NA |
| 4 | 353 | 0.58 | 0.76 | 47 | QM5, NA |
| 5 | 323 | 0.55 | 0.74 | 37 | 1PE |
Interfaces
3 interfaces between chains.
- A–B · 1202 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1195 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1173 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6ZL4 · 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 6ZL4 · PDBe 6ZL4 · UniProt Q5JID0
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