Research workbench
Shigella effector kinase ospg bound to amppnp and E2-ub UBCH7-ub conjugate
Analyse Shigella effector kinase ospg bound to amppnp and E2-ub UBCH7-ub conjugate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Q5H
- Type
- protein
- Length
- 400 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein kinase ospg; Polyubiquitin; Ubiquitin-conjugating enzyme E2 L3
- EC
- 2.7.-.-, 6.3.2.19
- UniProt
- Q3YTH2, P0CG63, P68036
- Ligands
- ANP, MG
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein kinase ospg (EC 2.7.-.-) | protein | 169 | 41% helix, 28% strand | Q3YTH2 |
| B | Polyubiquitin (EC 6.3.2.19) | protein | 76 | 24% helix, 33% strand | P0CG63 |
| C | Ubiquitin-conjugating enzyme E2 L3 (EC 6.3.2.19) | protein | 155 | 37% helix, 20% strand | P68036 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 172 | 0.57 | 0.81 | 25 | empty |
| 2 | 193 | 0.54 | 0.78 | 24 | ANP |
| 3 | 82 | 0.53 | 0.84 | 20 | empty |
| 4 | 79 | 0.43 | 0.80 | 19 | empty |
| 5 | 74 | 0.35 | 0.76 | 15 | MG |
Interfaces
3 interfaces between chains.
- A–B · 810 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 669 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 279 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4Q5H · Shigella Effector Kinase OspG bound to AMPPNP and E2-Ub UbcH7-Ub Conjugate · the same entry in another collection · chain A against A, TM-score 1.00
- Q3YTH2 · AlphaFold monomer V2.0 prediction for protein kinase ospg (Q3YTH2) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P68036 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 L3 (P68036) · a predicted model of the same protein · chain C against A, TM-score 0.99
- P0CG63 · AlphaFold monomer V2.0 prediction for polyubiquitin (P0CG63) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q3YTH2
- Every structure of UniProt P0CG63
- Every structure of UniProt P68036
- Elsewhere: RCSB PDB 4Q5H · PDBe 4Q5H · UniProt Q3YTH2 · UniProt P0CG63 · UniProt P68036
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