MolNFT v1 · #117493 · protein
Crystal structure of substrate-bound glutamate transporter homologue glttk
5E9S · PROTON/GLUTAMATE symporter, sdf family: “Crystal structure of substrate-bound glutamate transporter homologue glttk”. X-ray diffraction, 2 ligands (ASP, NA), 20 pockets (best druggability 0.88). MolNFT v1 #117493 on GenesisL1: 3D…
- PDB
- 5E9S
- Type
- protein
- Length
- 1,280 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PROTON/GLUTAMATE symporter, sdf family
- UniProt
- Q5JID0
- Ligands
- ASP, NA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | PROTON/GLUTAMATE symporter, sdf family | protein | 427 | 78% helix, 0% strand | Q5JID0 |
| C | PROTON/GLUTAMATE symporter, sdf family | protein | 426 | 77% helix, 0% strand | Q5JID0 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 9 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 33 copies · chains A, B, C
- 1PE · Pentaethylene glycol · additive · 7 copies · chains A, C, B
- PGE · Triethylene glycol · additive · 7 copies · chains A, C, B
- P6G · Hexaethylene glycol · additive · 5 copies · chains A, B, C
- DMU · Decyl-beta-D-maltopyranoside · additive · 3 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.88 | 0.92 | 52 | PEG |
| 2 | 523 | 0.60 | 0.74 | 71 | 1PE, PEG, P6G |
| 3 | 451 | 0.58 | 0.73 | 63 | PEG, PGE |
| 4 | 346 | 0.54 | 0.73 | 48 | PEG, P6G |
| 5 | 158 | 0.43 | 0.73 | 18 | PEG |
Interfaces
3 interfaces between chains.
- A–C · 1195 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1184 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1136 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5E9S · Crystal structure of substrate-bound glutamate transporter homologue GltTk · the same entry in another collection · chain C against C, 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 5E9S · PDBe 5E9S · UniProt Q5JID0
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