MolNFT v1 · #47772 · protein
Crystal structure of putative dioxygenase (YP_555069.1) from burkholderia xenovorans LB400 at 1.40 a resolution
2P8I: “Crystal structure of putative dioxygenase (YP_555069.1) from burkholderia xenovorans LB400 at 1.40 a…”. X-ray diffraction, 2 ligands (CL, PO4), 6 pockets (best druggability 0.42). MolNFT v1 #47772 on GenesisL1: 3D structure, binding…
- PDB
- 2P8I
- Type
- protein
- Length
- 467 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative dioxygenase
- UniProt
- Q13JM0
- Ligands
- CL, PO4
- Pockets
- 6 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Putative dioxygenase | protein | 117 | 38% helix, 23% strand | Q13JM0 |
| C | Putative dioxygenase | protein | 116 | 35% helix, 23% strand | Q13JM0 |
Ligands and binding sites
- CL · Chloride ion · ion · 4 copies · chains A, B, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
- CIT · Citric acid · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.42 | 0.73 | 26 | empty |
| 2 | 86 | 0.39 | 0.77 | 19 | CL |
| 3 | 69 | 0.39 | 0.79 | 18 | empty |
| 4 | 64 | 0.39 | 0.80 | 19 | empty |
| 5 | 64 | 0.35 | 0.78 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1392 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1384 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 518 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 2P8I · 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 2P8I · PDBe 2P8I · UniProt Q13JM0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.