MolNFT v1 · #105067 · protein
1.65 ångström resolution crystal structure of betaine aldehyde dehydrogenase (betb) from staphylococcus aureus with bme-modified CYS289 and peg molecule in active site
4QTO: “1.65 ångström resolution crystal structure of betaine aldehyde dehydrogenase (betb) from staphylococcus…”. X-ray diffraction, 1 ligand (NA), 17 pockets (best druggability 0.84). MolNFT v1 #105067 on GenesisL1: 3D structure, binding…
- PDB
- 4QTO
- Type
- protein
- Length
- 1,985 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
- 17 · best druggability 0.84
Structure
x-ray diffraction · 3 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 | 497 | 41% helix, 21% strand | Q5HCU0 |
| C | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 496 | 41% helix, 21% strand | Q5HCU0 |
| D | Betaine aldehyde dehydrogenase (EC 1.2.1.8) | protein | 495 | 41% helix, 21% strand | Q5HCU0 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 6 copies · chains A, B, D
- PGE · Triethylene glycol · additive · 5 copies · chains A, B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains C
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.84 | 0.93 | 63 | NA |
| 2 | 432 | 0.84 | 0.92 | 56 | NA |
| 3 | 267 | 0.77 | 0.90 | 54 | empty |
| 4 | 223 | 0.76 | 0.91 | 44 | empty |
| 5 | 150 | 0.73 | 0.92 | 32 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3895 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 3866 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 818 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 790 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 760 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 1 covalent (artifact, additive adduct).
Compared structures
- 4QTO · 1.65 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 4QTO · PDBe 4QTO · UniProt Q5HCU0
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