Research workbench
Crystal structure of Serine Racemase from Dictyostelium discoideum.
Analyse Crystal structure of Serine Racemase from Dictyostelium discoideum. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LUT
- Type
- protein
- Length
- 611 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.35
- Source
- Dictyostelium discoideum
- Molecule
- Probable serine racemase
- EC
- 4.3.1.17, 4.3.1.18, 5.1.1.18
- UniProt
- Q54HH2
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · resolution 1.35 · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable serine racemase (EC 4.3.1.17, 4.3.1.18, 5.1.1.18) | protein | 307 | 51% helix, 16% strand | Q54HH2 |
| B | Probable serine racemase (EC 4.3.1.17, 4.3.1.18, 5.1.1.18) | protein | 304 | 50% helix, 16% strand | Q54HH2 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.62 | 0.78 | 39 | empty |
| 2 | 364 | 0.61 | 0.77 | 43 | empty |
| 3 | 194 | 0.46 | 0.74 | 26 | empty |
| 4 | 177 | 0.46 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 727 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (cofactor).
Compared structures
- 6LUT · Crystal structure of serine racemase from dictyostelium discoideum. · the same entry in another collection · chain A against A, TM-score 1.00
- Q54HH2 · AlphaFold monomer V2.0 prediction for probable serine racemase (Q54HH2) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q54HH2
- Elsewhere: RCSB PDB 6LUT · PDBe 6LUT · UniProt Q54HH2
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