MolNFT v1 · #71899 · protein
Crystal structure of human gamma-BUTYROBETAINE,2-oxoglutarate dioxygenase 1 (BBOX1)
3MS5 · Gamma-butyrobetaine dioxygenase: “Crystal structure of human gamma-BUTYROBETAINE,2-oxoglutarate dioxygenase 1 (BBOX1)”. X-ray diffraction, 4 ligands (OGA, REE, NI), 2 pockets (best druggability 0.79). MolNFT v1 #71899 on GenesisL1…
- PDB
- 3MS5
- Type
- protein
- Length
- 385 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-butyrobetaine dioxygenase
- EC
- 1.14.11.1
- UniProt
- O75936
- Ligands
- OGA, REE, NI, ZN
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) | protein | 385 | 30% helix, 29% strand | O75936 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · chains A
- REE · 2-(2-carboxyethyl)-1,1,1-trimethyldiazanium · ligand · chains A
- NI · Nickel (II) ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.79 | 0.94 | 37 | NI, OGA, REE, EDO |
| 2 | 155 | 0.42 | 0.74 | 21 | EDO |
Compared structures
- 3MS5 · Crystal Structure of Human gamma-butyrobetaine,2-oxoglutarate dioxygenase 1 (BBOX1) · the same entry in another collection · chain A against A, TM-score 1.00
- O75936 · AlphaFold monomer V2.0 prediction for gamma-butyrobetaine dioxygenase (O75936) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O75936
- Elsewhere: RCSB PDB 3MS5 · PDBe 3MS5 · UniProt O75936
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