Research workbench
Crystal structure of the tpr domain of xanthomonas campestris ybgf
Analyse Crystal structure of the tpr domain of xanthomonas campestris ybgf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XEV
- Type
- protein
- Length
- 367 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ybgf
- UniProt
- Q8P6F4
- Ligands
- ZN, CL
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ybgf | protein | 121 | 77% helix, 0% strand | Q8P6F4 |
| B | Ybgf | protein | 124 | 77% helix, 0% strand | Q8P6F4 |
| C | Ybgf | protein | 122 | 78% helix, 0% strand | Q8P6F4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.70 | 0.98 | 24 | empty |
| 2 | 131 | 0.46 | 0.77 | 19 | empty |
| 3 | 113 | 0.37 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 640 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 608 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2XEV · Crystal structure of the TPR domain of Xanthomonas campestris ybgF · 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 Q8P6F4
- Elsewhere: RCSB PDB 2XEV · PDBe 2XEV · UniProt Q8P6F4
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