Research workbench
Crystal structure of putative dioxygenase (YP_555069.1) from burkholderia xenovorans LB400 at 1.70 a resolution
Analyse Crystal structure of putative dioxygenase (YP_555069.1) from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NYH
- Type
- protein
- Length
- 231 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dioxygenase
- UniProt
- Q13JM0
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative dioxygenase | protein | 116 | 37% helix, 23% strand | Q13JM0 |
| B | Putative dioxygenase | protein | 115 | 38% helix, 23% strand | Q13JM0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.40 | 0.78 | 23 | empty |
| 2 | 56 | 0.33 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1400 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 2NYH · Crystal structure of putative dioxygenase (YP_555069.1) from Burkholderia Xenovorans… · 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 Q13JM0
- Elsewhere: RCSB PDB 2NYH · PDBe 2NYH · UniProt Q13JM0
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