Research workbench
Crystal structure of short-chain dehydrogenase from rhodopseudomonas palustris
Analyse Crystal structure of short-chain dehydrogenase from rhodopseudomonas palustris in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3H7A
- Type
- protein
- Length
- 849 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain dehydrogenase
- UniProt
- Q6NDT3
- Ligands
- UNL
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Short chain dehydrogenase | protein | 212 | 54% helix, 21% strand | Q6NDT3 |
| B | Short chain dehydrogenase | protein | 213 | 52% helix, 21% strand | Q6NDT3 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 3 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 963 | 0.78 | 0.80 | 84 | UNL |
| 2 | 126 | 0.48 | 0.79 | 18 | empty |
| 3 | 138 | 0.47 | 0.78 | 18 | empty |
| 4 | 120 | 0.46 | 0.78 | 16 | empty |
| 5 | 114 | 0.43 | 0.77 | 21 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1684 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1670 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 869 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 844 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3H7A · CRYSTAL STRUCTURE OF SHORT-CHAIN DEHYDROGENASE FROM Rhodopseudomonas palustris · 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 Q6NDT3
- Elsewhere: RCSB PDB 3H7A · PDBe 3H7A · UniProt Q6NDT3
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