Research workbench
Crystal structure of a short-chain DEHYDROGENASE/REDUCTASE from vibrio parahaemolyticus
Analyse Crystal structure of a short-chain DEHYDROGENASE/REDUCTASE from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GUY
- Type
- protein
- Length
- 1,685 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- A6B7Q2
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 204 | 46% helix, 19% strand | A6B7Q2 |
| B | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 204 | 45% helix, 20% strand | A6B7Q2 |
| C | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 212 | 45% helix, 19% strand | A6B7Q2 |
| D | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 220 | 44% helix, 18% strand | A6B7Q2 |
| G | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 228 | 42% helix, 17% strand | A6B7Q2 |
| H | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 209 | 46% helix, 20% strand | A6B7Q2 |
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 742 | 0.79 | 0.83 | 114 | empty |
| 2 | 556 | 0.75 | 0.83 | 80 | empty |
| 3 | 223 | 0.65 | 0.84 | 40 | empty |
| 4 | 131 | 0.61 | 0.86 | 36 | empty |
| 5 | 193 | 0.60 | 0.82 | 35 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1625 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1607 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1601 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1589 Ų buried · 11 hydrogen bonds · protein-protein
- E–G · 1077 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3GUY · Crystal structure of a short-chain dehydrogenase/reductase from Vibrio parahaemolyticus · 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 A6B7Q2
- Elsewhere: RCSB PDB 3GUY · PDBe 3GUY · UniProt A6B7Q2
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