MolNFT v1 · #134707 · protein
Crystal structure of catechol 1,2-dioxygenase from burkholderia vietnamiensis
5TD3: “Crystal structure of catechol 1,2-dioxygenase from burkholderia vietnamiensis”. X-ray diffraction, 4 ligands (PTY, ZN, MG), 11 pockets (best druggability 0.85). MolNFT v1 #134707 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5TD3
- Type
- protein
- Length
- 611 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol 1,2-dioxygenase
- EC
- 1.13.11.1
- UniProt
- A4JR51
- Ligands
- PTY, ZN, MG, CL
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol 1,2-dioxygenase (EC 1.13.11.1) | protein | 307 | 29% helix, 21% strand | A4JR51 |
| B | Catechol 1,2-dioxygenase (EC 1.13.11.1) | protein | 304 | 28% helix, 21% strand | A4JR51 |
Ligands and binding sites
- PTY · Phosphatidylethanolamine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.85 | 0.85 | 56 | PTY |
| 2 | 61 | 0.70 | 0.96 | 19 | empty |
| 3 | 59 | 0.67 | 0.95 | 18 | empty |
| 4 | 81 | 0.56 | 0.87 | 19 | empty |
| 5 | 78 | 0.52 | 0.85 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3598 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 5TD3 · Crystal structure of Catechol 1,2-dioxygenase from Burkholderia vietnamiensis · 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 A4JR51
- Elsewhere: RCSB PDB 5TD3 · PDBe 5TD3 · UniProt A4JR51
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.