Research workbench
The crystal structure of short chain dehydrogenase from rhodobacter sphaeroides
Analyse The crystal structure of short chain dehydrogenase from rhodobacter sphaeroides in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UXY
- Type
- protein
- Length
- 963 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- Q3IVH6
- Ligands
- NAD
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 241 | 48% helix, 16% strand | Q3IVH6 |
| B | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 243 | 49% helix, 15% strand | Q3IVH6 |
| D | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 238 | 47% helix, 18% strand | Q3IVH6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.86 | 0.87 | 81 | empty |
| 2 | 544 | 0.74 | 0.82 | 49 | NAD |
| 3 | 464 | 0.71 | 0.81 | 45 | empty |
| 4 | 486 | 0.69 | 0.79 | 44 | empty |
| 5 | 444 | 0.66 | 0.78 | 42 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1548 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1519 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1312 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1302 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 60 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 3UXY · The crystal structure of short chain dehydrogenase from Rhodobacter sphaeroides · 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 Q3IVH6
- Elsewhere: RCSB PDB 3UXY · PDBe 3UXY · UniProt Q3IVH6
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