Research workbench
Crystal structure of gltph R397A in sodium-bound state
Analyse Crystal structure of gltph R397A in sodium-bound state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OYF
- Type
- protein
- Length
- 2,394 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamate symport protein
- Ligands
- NA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glutamate symport protein | protein | 399 | 79% helix, 0% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · 6 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 694 | 0.88 | 0.92 | 54 | empty |
| 2 | 687 | 0.88 | 0.91 | 48 | empty |
| 3 | 370 | 0.56 | 0.74 | 60 | empty |
| 4 | 293 | 0.53 | 0.74 | 38 | empty |
| 5 | 298 | 0.52 | 0.74 | 43 | empty |
Interfaces
9 interfaces between chains.
- E–F · 1130 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1127 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1126 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 1121 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 1119 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4OYF · Crystal structure of GLTPH R397A IN Sodium-bound state · 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
- Elsewhere: RCSB PDB 4OYF · PDBe 4OYF
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