Research workbench
Crystal structure of a putative dioxygenase (npun_f5605) from nostoc punctiforme pcc 73102 at 2.60 A resolution
Analyse Crystal structure of a putative dioxygenase (npun_f5605) from nostoc… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QDR
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Nostoc punctiforme
- Molecule
- Uncharacterized protein
- Ligands
- UNL
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.6 · 2 distinct chains · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 285 | 3% helix, 46% strand | — |
| B | Uncharacterized protein | protein | 284 | 2% helix, 45% strand | — |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.79 | 0.97 | 31 | UNL |
| 2 | 112 | 0.78 | 0.96 | 26 | UNL |
| 3 | 58 | 0.52 | 0.87 | 22 | empty |
| 4 | 130 | 0.44 | 0.76 | 27 | empty |
| 5 | 84 | 0.34 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 842 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified, 1 covalent (engineered, covalent ligand).
Compared structures
- 2QDR · Crystal structure of a putative dioxygenase (NPUN_F5605) from nostoc punctiforme pcc… · 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
- Elsewhere: RCSB PDB 2QDR · PDBe 2QDR
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