MolNFT v1 · #123589 · protein
Structure of xanthomonas campestris effector protein xopd bound to ubiquitin
5JP3 · Xanthomonas outer protein D: “Structure of xanthomonas campestris effector protein xopd bound to ubiquitin”. X-ray diffraction, 1 ligand (AYE), 17 pockets (best druggability 0.72). MolNFT v1 #123589 on GenesisL1: 3D structure…
- PDB
- 5JP3
- Type
- protein
- Length
- 1,090 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xanthomonas outer protein D; Polyubiquitin-B
- UniProt
- Q3BYJ5, P0CG47
- Ligands
- AYE
- Pockets
- 17 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xanthomonas outer protein D | protein | 205 | 41% helix, 15% strand | Q3BYJ5 |
| C, G | Xanthomonas outer protein D | protein | 196 | 43% helix, 15% strand | Q3BYJ5 |
| E | Xanthomonas outer protein D | protein | 193 | 41% helix, 16% strand | Q3BYJ5 |
| B, D, H, F | Polyubiquitin-B | protein | 75 | 16% helix, 36% strand | P0CG47 |
Ligands and binding sites
- AYE · prop-2-en-1-amine · ligand · 4 copies · chains A, B, C, D, H, G, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.72 | 0.83 | 59 | empty |
| 2 | 256 | 0.59 | 0.79 | 28 | empty |
| 3 | 215 | 0.57 | 0.79 | 36 | empty |
| 4 | 199 | 0.57 | 0.79 | 34 | empty |
| 5 | 204 | 0.53 | 0.77 | 36 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1099 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 965 Ų buried · 23 hydrogen bonds · protein-protein
- H–G · 944 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 838 Ų buried · 22 hydrogen bonds · protein-protein
- C–G · 406 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 5JP3 · Structure of Xanthomonas campestris effector protein XopD bound to ubiquitin · 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 P0CG47
- Elsewhere: RCSB PDB 5JP3 · PDBe 5JP3 · UniProt Q3BYJ5 · UniProt P0CG47
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