Research workbench
Fingerprint and structural analysis of a apo scor enzyme from clostridium thermocellum
Analyse Fingerprint and structural analysis of a apo scor enzyme from clostridium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GED
- Type
- protein
- Length
- 485 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- A3DFK9
- Ligands
- THJ, NA
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 242 | 46% helix, 16% strand | A3DFK9 |
| B | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 243 | 45% helix, 16% strand | A3DFK9 |
Ligands and binding sites
- THJ · Thiosulfate · ligand · 3 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 289 | 0.55 | 0.76 | 36 | GOL |
| 2 | 279 | 0.54 | 0.76 | 35 | GOL |
| 3 | 117 | 0.38 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1408 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 3GED · Fingerprint and Structural Analysis of a Apo SCOR enzyme from Clostridium thermocellum · 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 A3DFK9
- Elsewhere: RCSB PDB 3GED · PDBe 3GED · UniProt A3DFK9
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