Research workbench
Crystal structure analysis of the 2,3-dioxygenase lapb from pseudomonas in the complex with 4-methylcatechol
Analyse Crystal structure analysis of the 2,3-dioxygenase lapb from pseudomonas in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HPY
- Type
- protein
- Length
- 1,168 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catechol 2,3-dioxygenase
- EC
- 1.13.11.2
- UniProt
- Q7WYF5
- Ligands
- MCT, FE
- Pockets
- 11 · best druggability 0.91
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 288 | 18% helix, 38% strand | Q7WYF5 |
| C, D | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 296 | 20% helix, 38% strand | Q7WYF5 |
Ligands and binding sites
- MCT · 4-methylcatechol · ligand · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.91 | 0.93 | 130 | empty |
| 2 | 60 | 0.69 | 0.97 | 24 | empty |
| 3 | 54 | 0.69 | 0.97 | 23 | empty |
| 4 | 127 | 0.67 | 0.89 | 34 | empty |
| 5 | 92 | 0.66 | 0.91 | 21 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2221 Ų buried · 43 hydrogen bonds · protein-protein
- A–D · 2214 Ų buried · 42 hydrogen bonds · protein-protein
- C–D · 907 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 516 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3HPY · Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas in the complex… · 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 Q7WYF5
- Elsewhere: RCSB PDB 3HPY · PDBe 3HPY · UniProt Q7WYF5
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