MolNFT v1 · #66427 · protein
Crystal structure analysis of the 2,3-dioxygenase lapb from pseudomonas in complex with a product
3HQ0 · Catechol 2,3-dioxygenase: “Crystal structure analysis of the 2,3-dioxygenase lapb from pseudomonas in complex with a product”. X-ray diffraction, 2 ligands (M3P, FE), 12 pockets (best druggability 0.91). MolNFT v1 #66427 on…
- PDB
- 3HQ0
- Type
- protein
- Length
- 1,169 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
- M3P, FE
- Pockets
- 12 · best druggability 0.91
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 297 | 19% helix, 37% strand | Q7WYF5 |
| B, D | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 288 | 19% helix, 38% strand | Q7WYF5 |
| C | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 296 | 20% helix, 36% strand | Q7WYF5 |
Ligands and binding sites
- M3P · (2E,4E)-2-hydroxy-6-oxohepta-2,4-dienoic acid · ligand · 3 copies · chains B, C, D
- 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
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1111 | 0.91 | 0.94 | 136 | empty |
| 2 | 58 | 0.69 | 0.97 | 23 | empty |
| 3 | 54 | 0.68 | 0.97 | 24 | empty |
| 4 | 111 | 0.67 | 0.90 | 41 | empty |
| 5 | 120 | 0.67 | 0.89 | 33 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2184 Ų buried · 42 hydrogen bonds · protein-protein
- A–D · 2118 Ų buried · 37 hydrogen bonds · protein-protein
- C–D · 687 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 551 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 524 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3HQ0 · Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas in complex with a… · 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 3HQ0 · PDBe 3HQ0 · UniProt Q7WYF5
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