MolNFT v1 · #115317 · protein
Crystal structure of gltph R397A in complex with na+ and L-asp
5CFY · 425AA long hypothetical proton glutamate symport protein: “Crystal structure of gltph R397A in complex with na+ and L-asp”. X-ray diffraction, 2 ligands (ASP, NA), 20 pockets (best druggability 0.89). MolNFT v1 #115317 on GenesisL1…
- PDB
- 5CFY
- Type
- protein
- Length
- 2,466 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 425AA long hypothetical proton glutamate symport protein
- UniProt
- O59010
- Ligands
- ASP, NA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 425AA long hypothetical proton glutamate symport protein | protein | 411 | 73% helix, 0% strand | O59010 |
Ligands and binding sites
- ASP · Aspartic acid · ligand · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · 12 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.89 | 0.92 | 45 | empty |
| 2 | 697 | 0.89 | 0.92 | 44 | empty |
| 3 | 380 | 0.56 | 0.74 | 56 | empty |
| 4 | 278 | 0.54 | 0.76 | 45 | empty |
| 5 | 289 | 0.54 | 0.74 | 35 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1134 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1125 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1120 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1117 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 1112 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5CFY · Crystal structure of gltph R397A in complex with na+ and L-asp · the same entry in another collection · chain F against F, TM-score 1.00
- O59010 · AlphaFold monomer V2.0 prediction for glutamate transporter homolog (O59010) · a predicted model of the same protein · chain E against A, TM-score 0.98
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 O59010
- Elsewhere: RCSB PDB 5CFY · PDBe 5CFY · UniProt O59010
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