Research workbench
Crystal structure of the glutamate transporter homologue glttk in complex with D-aspartate
Analyse Crystal structure of the glutamate transporter homologue glttk in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R7R
- Type
- protein
- Length
- 1,244 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PROTON/GLUTAMATE symporter, sdf family
- UniProt
- Q5JID0
- Ligands
- DAS, NA
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PROTON/GLUTAMATE symporter, sdf family | protein | 416 | 78% helix, 0% strand | Q5JID0 |
| B | PROTON/GLUTAMATE symporter, sdf family | protein | 406 | 80% helix, 0% strand | Q5JID0 |
| C | PROTON/GLUTAMATE symporter, sdf family | protein | 422 | 77% helix, 0% strand | Q5JID0 |
Ligands and binding sites
- DAS · D-aspartic acid · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 9 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 3 copies · chains A, B, C
- P6G · Hexaethylene glycol · additive · 2 copies · chains B
- PG4 · Tetraethylene glycol · additive · chains A
- DMU · Decyl-beta-D-maltopyranoside · additive · chains A
- 1PE · Pentaethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.88 | 0.92 | 43 | PGE |
| 2 | 551 | 0.62 | 0.74 | 74 | P6G |
| 3 | 469 | 0.59 | 0.74 | 62 | PEG, PGE |
| 4 | 394 | 0.57 | 0.74 | 60 | empty |
| 5 | 157 | 0.43 | 0.73 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1237 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1221 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1170 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6R7R · Crystal structure of the glutamate transporter homologue GltTk in complex with D-aspartate · 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 6R7R · PDBe 6R7R · UniProt Q5JID0
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