MolNFT v1 · #100184 · protein
1.85 ångström resolution crystal structure of betaine aldehyde dehydrogenase (betb) from staphylococcus aureus (IDP00699) in complex with NAD+
4MPY: “1.85 ångström resolution crystal structure of betaine aldehyde dehydrogenase (betb) from staphylococcus…”. X-ray diffraction, 2 ligands (NAD, NA), 20 pockets (best druggability 0.88). MolNFT v1 #100184 on GenesisL1: 3D structure…
- PDB
- 4MPY
- Type
- protein
- Length
- 4,003 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Betaine aldehyde dehydrogenase
- EC
- 1.2.1.8
- UniProt
- Q5HCU0
- Ligands
- NAD, NA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, H | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 500 | 42% helix, 21% strand | Q5HCU0 |
| C, G | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 503 | 42% helix, 20% strand | Q5HCU0 |
| D, F | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 498 | 41% helix, 20% strand | Q5HCU0 |
| E | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 501 | 42% helix, 21% strand | Q5HCU0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NA · Sodium ion · metal · 19 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.88 | 0.91 | 103 | NA |
| 2 | 510 | 0.85 | 0.91 | 68 | NA |
| 3 | 476 | 0.84 | 0.91 | 56 | NA |
| 4 | 446 | 0.84 | 0.91 | 59 | NA |
| 5 | 525 | 0.84 | 0.90 | 83 | empty |
Interfaces
19 interfaces between chains.
- E–F · 3946 Ų buried · 59 hydrogen bonds · protein-protein
- G–H · 3928 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 3922 Ų buried · 59 hydrogen bonds · protein-protein
- C–D · 3912 Ų buried · 60 hydrogen bonds · protein-protein
- A–D · 797 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (artifact).
Compared structures
- 4MPY · 1.85 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from… · 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 Q5HCU0
- Elsewhere: RCSB PDB 4MPY · PDBe 4MPY · UniProt Q5HCU0
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