MolNFT v1 · #66422 · protein
Crystal structure analysis of the 2,3-dioxygenase lapb from pseudomonas sp. KL28
3HPV · Catechol 2,3-dioxygenase: “Crystal structure analysis of the 2,3-dioxygenase lapb from pseudomonas sp. KL28”. X-ray diffraction, 1 ligand (FE2), 11 pockets (best druggability 0.90). MolNFT v1 #66422 on GenesisL1: 3D structure…
- PDB
- 3HPV
- Type
- protein
- Length
- 1,161 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
- FE2
- Pockets
- 11 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 297 | 20% helix, 37% strand | Q7WYF5 |
| B, C, D | Catechol 2,3-dioxygenase (EC 1.13.11.2) | protein | 288 | 18% helix, 39% strand | Q7WYF5 |
Ligands and binding sites
- FE2 · Fe (II) 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 | 794 | 0.90 | 0.94 | 126 | empty |
| 2 | 304 | 0.84 | 0.94 | 36 | empty |
| 3 | 51 | 0.68 | 0.97 | 21 | empty |
| 4 | 113 | 0.65 | 0.89 | 36 | empty |
| 5 | 118 | 0.64 | 0.88 | 33 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2125 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 2057 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 593 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 591 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 453 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3HPV · Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas sp. KL28 · 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 3HPV · PDBe 3HPV · UniProt Q7WYF5
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