MolNFT v1 · #120231 · protein
NAD+ complex structure of aldehyde dehydrogenase from bacillus cereus
5GTK · Betaine-aldehyde dehydrogenase: “NAD+ complex structure of aldehyde dehydrogenase from bacillus cereus”. X-ray diffraction, 2 ligands (NAD, NA), 18 pockets (best druggability 0.83). MolNFT v1 #120231 on GenesisL1: 3D structure…
- PDB
- 5GTK
- Type
- protein
- Length
- 1,959 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Betaine-aldehyde dehydrogenase
- UniProt
- A0A150BLG9
- Ligands
- NAD, NA
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Betaine-aldehyde dehydrogenase | protein | 491 | 41% helix, 22% strand | A0A150BLG9 |
| B | Betaine-aldehyde dehydrogenase | protein | 488 | 42% helix, 21% strand | A0A150BLG9 |
| C | Betaine-aldehyde dehydrogenase | protein | 489 | 42% helix, 21% strand | A0A150BLG9 |
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, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.83 | 0.93 | 49 | empty |
| 2 | 261 | 0.81 | 0.93 | 48 | empty |
| 3 | 398 | 0.79 | 0.88 | 47 | empty |
| 4 | 444 | 0.78 | 0.87 | 42 | empty |
| 5 | 392 | 0.78 | 0.88 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–D · 2705 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 2648 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1147 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1141 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1077 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5GTK · NAD+ complex structure of aldehyde dehydrogenase from bacillus cereus · 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 A0A150BLG9
- Elsewhere: RCSB PDB 5GTK · PDBe 5GTK · UniProt A0A150BLG9
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