MolNFT v1 · #87270 · protein
Structure of shigella effector ospg in complex with host UBCH5C- ubiquitin conjugate
4BVU · Protein kinase ospg: “Structure of shigella effector ospg in complex with host UBCH5C- ubiquitin conjugate”. X-ray diffraction, 5 pockets (best druggability 0.59). MolNFT v1 #87270 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4BVU
- Type
- protein
- Length
- 393 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase ospg; Ubiquitin-conjugating enzyme E2 D3; Ubiquitin
- EC
- 2.7.-.-, 6.3.2.19
- UniProt
- Q99PZ6, P61077, P0CG48
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein kinase ospg (EC 2.7.-.-) | protein | 171 | 39% helix, 23% strand | Q99PZ6 |
| B | Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19) | protein | 146 | 36% helix, 18% strand | P61077 |
| C | Ubiquitin | protein | 76 | 20% helix, 30% strand | P0CG48 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 319 | 0.59 | 0.77 | 39 | empty |
| 2 | 192 | 0.55 | 0.79 | 24 | empty |
| 3 | 143 | 0.51 | 0.80 | 28 | empty |
| 4 | 62 | 0.33 | 0.77 | 14 | empty |
| 5 | 55 | 0.26 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 977 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 617 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 320 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4BVU · Structure of Shigella effector OspG in complex with host UbcH5c- Ubiquitin conjugate · the same entry in another collection · chain A against A, TM-score 1.00
- P61077 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D3 (P61077) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q99PZ6 · AlphaFold monomer V2.0 prediction for protein kinase ospg (Q99PZ6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q99PZ6
- Every structure of UniProt P61077
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 4BVU · PDBe 4BVU · UniProt Q99PZ6 · UniProt P61077 · UniProt P0CG48
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