Research workbench
Insight into the molecular determinants of thermal stability in halohydrin dehalogenase HHED2.
Analyse Insight into the molecular determinants of thermal stability in halohydrin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7B73
- Type
- protein
- Length
- 922 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- UniProt
- Q1YQT8
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 240 | 46% helix, 15% strand | Q1YQT8 |
| B | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 230 | 47% helix, 15% strand | Q1YQT8 |
| C | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 228 | 46% helix, 15% strand | Q1YQT8 |
| D | Short-chain DEHYDROGENASE/REDUCTASE sdr | protein | 224 | 48% helix, 15% strand | Q1YQT8 |
Ligands and binding sites
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.86 | 0.87 | 101 | GOL |
| 2 | 141 | 0.64 | 0.86 | 21 | NHE |
| 3 | 156 | 0.63 | 0.85 | 22 | NHE |
| 4 | 145 | 0.62 | 0.85 | 26 | NHE |
| 5 | 86 | 0.60 | 0.88 | 18 | NHE |
Interfaces
6 interfaces between chains.
- B–D · 1516 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1506 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1119 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 1101 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 139 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7B73 · Insight into the molecular determinants of thermal stability in halohydrin dehalogenase… · 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 Q1YQT8
- Elsewhere: RCSB PDB 7B73 · PDBe 7B73 · UniProt Q1YQT8
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