MolNFT v1 · #185314 · protein
Structure of SIDJ/CAM bound to sdea in pre-glutamylation state
7PPO · UBIQUITINATING/DEUBIQUITINATING enzyme sdea: “Structure of SIDJ/CAM bound to sdea in pre-glutamylation state”. Electron microscopy, 2 ligands (MG, CA), 20 pockets (best druggability 0.84). MolNFT v1 #185314 on GenesisL1: 3D…
- PDB
- 7PPO
- Type
- protein
- Length
- 1,383 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UBIQUITINATING/DEUBIQUITINATING enzyme sdea; Calmodulin-dependent glutamylase sidj…
- EC
- 3.4.22.-, 2.3.2.-, 2.4.2.31, 6.-.-.-
- UniProt
- Q5ZTK4, Q5ZTK6, P0DP24
- Ligands
- MG, CA
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 47% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-, 2.3.2.-, 2.4.2.31) | protein | 500 | 40% helix, 12% strand | Q5ZTK4 |
| C | Calmodulin-dependent glutamylase sidj (EC 6.-.-.-) | protein | 749 | 51% helix, 11% strand | Q5ZTK6 |
| B | Calmodulin | protein | 134 | 55% helix, 4% strand | P0DP24 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.84 | 0.85 | 96 | empty |
| 2 | 1130 | 0.80 | 0.81 | 110 | empty |
| 3 | 706 | 0.72 | 0.78 | 70 | empty |
| 4 | 54 | 0.72 | 0.98 | 15 | empty |
| 5 | 258 | 0.68 | 0.84 | 35 | empty |
Interfaces
2 interfaces between chains.
- A–C · 2485 Ų buried · 30 hydrogen bonds · protein-protein
- C–B · 1785 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 7PPO · Structure of SidJ/CaM bound to SdeA in pre-glutamylation state · the same entry in another collection · chain A against A, TM-score 1.00
- Q5ZTK6 · AlphaFold monomer V2.0 prediction for calmodulin-dependent glutamylase sidj (Q5ZTK6) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q5ZTK4 · AlphaFold monomer V2.0 prediction for UBIQUITINATING/DEUBIQUITINATING enzyme sdea (Q5ZTK4) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P0DP24 · AlphaFold monomer V2.0 prediction for calmodulin-2 (P0DP24) · a predicted model of the same protein · chain B against A, TM-score 0.41
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 Q5ZTK4
- Every structure of UniProt Q5ZTK6
- Every structure of UniProt P0DP24
- Elsewhere: RCSB PDB 7PPO · PDBe 7PPO · UniProt Q5ZTK4 · UniProt Q5ZTK6 · UniProt P0DP24
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