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Anaerobic crystal structure analysis of the 1,2-dihydroxynaphthalene dioxygenase from pseudomonas sp. strain C18 complexes with 2,3- dihydroxybiphenyl
Analyse Anaerobic crystal structure analysis of the 1,2-dihydroxynaphthalene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EI3
- Type
- protein
- Length
- 298 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1,2-dihydroxynaphthalene dioxygenase
- EC
- 1.13.11.-
- UniProt
- P0A108
- Ligands
- BPY, MG, FE2
- Pockets
- 1 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1,2-dihydroxynaphthalene dioxygenase (EC 1.13.11.-) | protein | 298 | 19% helix, 36% strand | P0A108 |
Ligands and binding sites
- BPY · Biphenyl-2,3-diol · ligand · 3 copies · chains A
- MG · Magnesium ion · metal · chains A
- FE2 · Fe (II) ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.68 | 0.88 | 38 | BPY, GOL |
Compared structures
- 2EI3 · Anaerobic Crystal Structure Analysis of the 1,2-dihydroxynaphthalene dioxygenase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A108 · AlphaFold monomer V2.0 prediction for 1,2-dihydroxynaphthalene dioxygenase (P0A108) · a predicted model of the same protein · 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 P0A108
- Elsewhere: RCSB PDB 2EI3 · PDBe 2EI3 · UniProt P0A108
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