Research workbench
Staphylopine dehydrogenase in the apo state
Analyse Staphylopine dehydrogenase in the apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H31
- Type
- protein
- Length
- 856 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DUF2338 domain-containing protein
- UniProt
- A0A1K7Y513
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DUF2338 domain-containing protein | protein | 428 | 47% helix, 15% strand | A0A1K7Y513 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.83 | 0.97 | 26 | 2PE |
| 2 | 230 | 0.79 | 0.92 | 29 | 2PE |
| 3 | 1080 | 0.78 | 0.80 | 94 | empty |
| 4 | 980 | 0.77 | 0.79 | 88 | empty |
| 5 | 222 | 0.67 | 0.84 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1529 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6H31 · Staphylopine dehydrogenase in the apo 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
- Every structure of UniProt A0A1K7Y513
- Elsewhere: RCSB PDB 6H31 · PDBe 6H31 · UniProt A0A1K7Y513
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