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Crystal structure of a putative dehydrogenase from sulfitobacter sp. (COG1028) (target efi-513936) in its apo form
Analyse Crystal structure of a putative dehydrogenase from sulfitobacter sp. (COG1028)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YQY
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dehydrogenase
- UniProt
- A3T0C9
- Ligands
- MG
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dehydrogenase | protein | 251 | 49% helix, 18% strand | A3T0C9 |
| B | Putative dehydrogenase | protein | 233 | 46% helix, 20% strand | A3T0C9 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 399 | 0.68 | 0.80 | 48 | empty |
| 2 | 317 | 0.54 | 0.75 | 40 | empty |
| 3 | 110 | 0.39 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 102 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 4YQY · Crystal Structure of a putative Dehydrogenase from Sulfitobacter sp. (COG1028) (TARGET… · 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 A3T0C9
- Elsewhere: RCSB PDB 4YQY · PDBe 4YQY · UniProt A3T0C9
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