Research workbench
Xanthomonas campestris putative ogt (XCC0866), apostructure
Analyse Xanthomonas campestris putative ogt (XCC0866), apostructure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VSY
- Type
- protein
- Length
- 1,094 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- XCC0866
- UniProt
- Q8PC69
- Ligands
- PR, CL
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | XCC0866 | protein | 547 | 51% helix, 10% strand | Q8PC69 |
Ligands and binding sites
- PR · Praseodymium ion · metal · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 3 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 869 | 0.72 | 0.77 | 88 | empty |
| 2 | 546 | 0.71 | 0.80 | 71 | empty |
| 3 | 636 | 0.68 | 0.77 | 53 | empty |
| 4 | 70 | 0.30 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 282 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2VSY · Xanthomonas campestris putative OGT (XCC0866), apostructure · 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 Q8PC69
- Elsewhere: RCSB PDB 2VSY · PDBe 2VSY · UniProt Q8PC69
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