MolNFT v1 · #46583 · protein
Crystal structure of a protein with a cupin-like fold and unknown function (BXE_C0505) from burkholderia xenovorans LB400 at 1.55 a resolution
2O8Q · Hypothetical protein: “Crystal structure of a protein with a cupin-like fold and unknown function (BXE_C0505) from burkholderia…”. X-ray diffraction, 1 ligand (NI), 3 pockets (best druggability 0.61). MolNFT v1 #46583 on GenesisL1…
- PDB
- 2O8Q
- Type
- protein
- Length
- 244 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein
- UniProt
- Q13HN3
- Ligands
- NI
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein | protein | 122 | 4% helix, 46% strand | Q13HN3 |
| B | Hypothetical protein | protein | 122 | 4% helix, 46% strand | Q13HN3 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.61 | 0.79 | 31 | NI, EDO |
| 2 | 272 | 0.61 | 0.79 | 28 | NI, EDO |
| 3 | 61 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1593 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 2O8Q · Crystal structure of a protein with a cupin-like fold and unknown function (BXE_C0505)… · 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 Q13HN3
- Elsewhere: RCSB PDB 2O8Q · PDBe 2O8Q · UniProt Q13HN3
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