Research workbench
Human gamma-butyrobetaine dioxygenase (BBOX1) in complex with NI(II) and N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine (AR692B)
Analyse Human gamma-butyrobetaine dioxygenase (BBOX1) in complex with NI(II) and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C8R
- Type
- protein
- Length
- 2,304 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gamma-butyrobetaine dioxygenase
- EC
- 1.14.11.1
- UniProt
- O75936
- Ligands
- 6YT, NI, ZN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) | protein | 384 | 29% helix, 32% strand | O75936 |
Ligands and binding sites
- 6YT · N-(3-hydroxypicolinoyl)-S-(pyridin-2-ylmethyl)-L-cysteine · ligand · 6 copies · chains A, B, C, D, E, F
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- ZN · Zinc ion · metal · 6 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.80 | 0.82 | 65 | EDO |
| 2 | 1136 | 0.80 | 0.81 | 75 | EDO |
| 3 | 1071 | 0.80 | 0.81 | 65 | EDO |
| 4 | 68 | 0.73 | 0.97 | 22 | empty |
| 5 | 766 | 0.73 | 0.78 | 65 | empty |
Interfaces
8 interfaces between chains.
- C–D · 3836 Ų buried · 59 hydrogen bonds · protein-protein
- E–F · 3835 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 3760 Ų buried · 52 hydrogen bonds · protein-protein
- C–E · 444 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 194 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4C8R · Human gamma-butyrobetaine dioxygenase (BBOX1) in complex with Ni(II) and… · the same entry in another collection · chain D against D, 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 0.95
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 4C8R · PDBe 4C8R · UniProt O75936
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