Research workbench
Crystal structure of a short chain alcohol dehydrogenase-related dehydrogenase (target id nysgrc-011812) from sinorhizobium meliloti 1021 in space group P21
Analyse Crystal structure of a short chain alcohol dehydrogenase-related dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H15
- Type
- protein
- Length
- 1,044 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain alcohol dehydrogenase-related dehydrogenase
- EC
- 1.1.1.-
- UniProt
- Q92YJ2
- Ligands
- CA, CL
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Short chain alcohol dehydrogenase-related dehydrogenase (EC 1.1.1.-) | protein | 261 | 48% helix, 14% strand | Q92YJ2 |
Ligands and binding sites
- CA · Calcium ion · metal · 11 copies · chains A, B, C, D
- CL · Chloride ion · ion · 40 copies · chains A, D, C, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 862 | 0.88 | 0.90 | 77 | CL, CA |
| 2 | 600 | 0.74 | 0.81 | 52 | CL, MPD |
| 3 | 666 | 0.73 | 0.80 | 52 | CL, MPD |
| 4 | 731 | 0.73 | 0.78 | 51 | CA, CL, MPD |
| 5 | 673 | 0.71 | 0.78 | 54 | CL, MPD |
Interfaces
6 interfaces between chains.
- A–D · 1813 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1788 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1457 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1441 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 263 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4H15 · Crystal Structure of a short chain alcohol dehydrogenase-related dehydrogenase (target ID… · 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 Q92YJ2
- Elsewhere: RCSB PDB 4H15 · PDBe 4H15 · UniProt Q92YJ2
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