Research workbench
1.72 ångström resolution crystal structure of betaine aldehyde dehydrogenase (betb) P449M point mutant from staphylococcus aureus in complex with NAD+ and bme-modified CYS289
Analyse 1.72 ångström resolution crystal structure of betaine aldehyde dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EYU
- Type
- protein
- Length
- 1,964 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Betaine aldehyde dehydrogenase
- EC
- 1.2.1.8
- UniProt
- Q9L4P8
- Ligands
- NAD, NA
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 491 | 41% helix, 21% strand | Q9L4P8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.85 | 0.90 | 112 | empty |
| 2 | 394 | 0.84 | 0.92 | 49 | NA |
| 3 | 414 | 0.83 | 0.92 | 55 | NA |
| 4 | 696 | 0.78 | 0.83 | 79 | empty |
| 5 | 252 | 0.76 | 0.90 | 51 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3865 Ų buried · 59 hydrogen bonds · protein-protein
- A–B · 3847 Ų buried · 60 hydrogen bonds · protein-protein
- A–C · 807 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 775 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 767 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- 5EYU · 1.72 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) P449M… · 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 Q9L4P8
- Elsewhere: RCSB PDB 5EYU · PDBe 5EYU · UniProt Q9L4P8
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