Research workbench
2.25 ångström resolution crystal structure of betaine aldehyde dehydrogenase (betb) Y450L point mutant from staphylococcus aureus in complex with NAD+ and bme-modified CYS289
Analyse 2.25 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
- 5DIB
- Type
- protein
- Length
- 1,988 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
- 17 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 498 | 41% helix, 21% strand | Q9L4P8 |
| B, D | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 496 | 42% helix, 21% strand | Q9L4P8 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 683 | 0.87 | 0.91 | 102 | empty |
| 2 | 392 | 0.84 | 0.92 | 52 | NA |
| 3 | 342 | 0.78 | 0.88 | 59 | empty |
| 4 | 277 | 0.77 | 0.90 | 54 | empty |
| 5 | 260 | 0.77 | 0.90 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3936 Ų buried · 65 hydrogen bonds · protein-protein
- C–D · 3918 Ų buried · 65 hydrogen bonds · protein-protein
- A–C · 799 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 778 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 763 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact).
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 5DIB · PDBe 5DIB · UniProt Q9L4P8
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