Research workbench
Structure of xanthomonas campestris effector protein xopd bound to tomato sumo
Analyse Structure of xanthomonas campestris effector protein xopd bound to tomato sumo in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JP1
- Type
- protein
- Length
- 276 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthomonas outer protein D; Small ubiquitin-related modifier
- UniProt
- Q3BYJ5, Q9SMD1
- Ligands
- AYE, D1D
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xanthomonas outer protein D | protein | 199 | 40% helix, 15% strand | Q3BYJ5 |
| B | Small ubiquitin-related modifier | protein | 77 | 18% helix, 36% strand | Q9SMD1 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · chains A, B
- D1D · (4S,5S)-1,2-dithiane-4,5-diol · ligand · chains A
- MLI · Malonate ion · additive · 2 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.53 | 0.81 | 23 | MLI |
| 2 | 81 | 0.43 | 0.80 | 16 | empty |
| 3 | 136 | 0.43 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1226 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5JP1 · Structure of Xanthomonas campestris effector protein XopD bound to tomato SUMO · 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 Q3BYJ5
- Every structure of UniProt Q9SMD1
- Elsewhere: RCSB PDB 5JP1 · PDBe 5JP1 · UniProt Q3BYJ5 · UniProt Q9SMD1
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