Research workbench
Crystal structure of aldehyde dehydrogenase family protein from staphylococcus aureus
Analyse Crystal structure of aldehyde dehydrogenase family protein from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TY7
- Type
- protein
- Length
- 906 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aldehyde dehydrogenase SAV2122
- EC
- 1.2.1.3
- UniProt
- Q99SD6
- Ligands
- MG
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative aldehyde dehydrogenase SAV2122 (EC 1.2.1.3) | protein | 452 | 41% helix, 20% strand | Q99SD6 |
| B | Putative aldehyde dehydrogenase SAV2122 (EC 1.2.1.3) | protein | 454 | 42% helix, 21% strand | Q99SD6 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.80 | 0.82 | 109 | GOL |
| 2 | 396 | 0.66 | 0.79 | 46 | empty |
| 3 | 72 | 0.39 | 0.79 | 16 | empty |
| 4 | 63 | 0.34 | 0.77 | 15 | empty |
| 5 | 58 | 0.27 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1663 Ų buried · 36 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 3TY7 · Crystal Structure of Aldehyde Dehydrogenase family Protein from Staphylococcus aureus · the same entry in another collection · chain A against A, TM-score 1.00
- Q99SD6 · AlphaFold monomer V2.0 prediction for putative aldehyde dehydrogenase (Q99SD6) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q99SD6
- Elsewhere: RCSB PDB 3TY7 · PDBe 3TY7 · UniProt Q99SD6
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