Research workbench
Crystal structure of glycerate dehydrogenase related protein from thermoplasma acidophilum
Analyse Crystal structure of glycerate dehydrogenase related protein from thermoplasma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GVX
- Type
- protein
- Length
- 571 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycerate dehydrogenase related protein
- EC
- 1.1.1.2
- UniProt
- Q9HJV5
- Ligands
- K
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycerate dehydrogenase related protein (EC 1.1.1.2) | protein | 281 | 33% helix, 17% strand | Q9HJV5 |
| B | Glycerate dehydrogenase related protein (EC 1.1.1.2) | protein | 290 | 31% helix, 16% strand | Q9HJV5 |
Ligands and binding sites
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 322 | 0.57 | 0.76 | 28 | empty |
| 2 | 216 | 0.54 | 0.78 | 34 | empty |
| 3 | 265 | 0.50 | 0.74 | 36 | empty |
| 4 | 141 | 0.44 | 0.76 | 21 | empty |
| 5 | 90 | 0.33 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2417 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3GVX · Crystal structure of Glycerate dehydrogenase related protein from Thermoplasma acidophilum · 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 Q9HJV5
- Elsewhere: RCSB PDB 3GVX · PDBe 3GVX · UniProt Q9HJV5
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