Research workbench
Glutamate transporter homologue glttk in complex with a photo cage compound
Analyse Glutamate transporter homologue glttk in complex with a photo cage compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZGB
- Type
- protein
- Length
- 1,271 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PROTON/GLUTAMATE symporter, sdf family
- UniProt
- Q5JID0
- Ligands
- QJW
- Pockets
- 17 · best druggability 0.88
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 | 425 | 78% helix, 0% strand | Q5JID0 |
| B, C | PROTON/GLUTAMATE symporter, sdf family | protein | 423 | 78% helix, 0% strand | Q5JID0 |
Ligands and binding sites
- QJW · (2~{S},3~{S})-2-azanyl-3-[(2-nitrophenyl) methoxy]butanedioic acid · ligand · 3 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C
- PGE · Triethylene 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 636 | 0.88 | 0.92 | 53 | PEG |
| 2 | 481 | 0.63 | 0.76 | 55 | QJW |
| 3 | 393 | 0.62 | 0.77 | 44 | QJW |
| 4 | 449 | 0.60 | 0.75 | 54 | QJW |
| 5 | 320 | 0.56 | 0.75 | 42 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1200 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1195 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1149 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6ZGB · glutamate transporter homologue Glttk in complex with a photo cage compound · 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 6ZGB · PDBe 6ZGB · UniProt Q5JID0
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