MolNFT v1 · #104731 · protein
1.85 ångström resolution crystal structure of apo betaine aldehyde dehydrogenase (betb) G234S mutant from staphylococcus aureus (IDP00699) with bme-free sulfinic acid form of CYS289
4QJE: “1.85 ångström resolution crystal structure of apo betaine aldehyde dehydrogenase (betb) G234S mutant from…”. X-ray diffraction, 1 ligand (NA), 18 pockets (best druggability 0.89). MolNFT v1 #104731 on GenesisL1: 3D structure…
- PDB
- 4QJE
- Type
- protein
- Length
- 1,978 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
- Q5HCU0
- Ligands
- NA
- Pockets
- 18 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 493 | 41% helix, 21% strand | Q5HCU0 |
| C, D | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 496 | 40% helix, 21% strand | Q5HCU0 |
Ligands and binding sites
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 3 copies · chains A, B, C, D
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 991 | 0.89 | 0.91 | 140 | NA |
| 2 | 756 | 0.87 | 0.91 | 123 | NA |
| 3 | 226 | 0.75 | 0.90 | 41 | empty |
| 4 | 193 | 0.72 | 0.89 | 28 | empty |
| 5 | 425 | 0.67 | 0.79 | 47 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3939 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 3879 Ų buried · 59 hydrogen bonds · protein-protein
- B–D · 811 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 789 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 778 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
- 4QJE · 1.85 Angstrom resolution crystal structure of apo betaine aldehyde dehydrogenase (betB)… · 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 4QJE · PDBe 4QJE · UniProt Q5HCU0
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