MolNFT v1 · #53118 · protein
Crystal structure of catechol 2,3-dioxygenase
2WL3: “Crystal structure of catechol 2,3-dioxygenase”. X-ray diffraction, 2 ligands (FE, CA), 7 pockets (best druggability 0.68). MolNFT v1 #53118 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WL3
- Type
- protein
- Length
- 1,138 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol 2,3-dioxygenase
- UniProt
- Q6REQ5
- Ligands
- FE, CA
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol 2,3-dioxygenase | protein | 287 | 18% helix, 33% strand | Q6REQ5 |
| B | Catechol 2,3-dioxygenase | protein | 287 | 20% helix, 33% strand | Q6REQ5 |
| C | Catechol 2,3-dioxygenase | protein | 284 | 18% helix, 33% strand | Q6REQ5 |
| D | Catechol 2,3-dioxygenase | protein | 280 | 19% helix, 33% strand | Q6REQ5 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.68 | 0.87 | 35 | GOL |
| 2 | 611 | 0.64 | 0.75 | 51 | CA |
| 3 | 267 | 0.54 | 0.76 | 31 | empty |
| 4 | 225 | 0.52 | 0.77 | 31 | empty |
| 5 | 274 | 0.49 | 0.73 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 652 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 568 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 299 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 modified (engineered).
Compared structures
- 2WL3 · crystal structure of catechol 2,3-dioxygenase · 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 Q6REQ5
- Elsewhere: RCSB PDB 2WL3 · PDBe 2WL3 · UniProt Q6REQ5
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