MolNFT v1 · #182164 · protein
Cryo-EM structure of sidj-sdea-cam reaction intermediate complex
7MIR · Calmodulin-dependent glutamylase sidj: “Cryo-EM structure of sidj-sdea-cam reaction intermediate complex”. Electron microscopy, 4 ligands (AMP, ATP, MG), 20 pockets (best druggability 0.83). MolNFT v1 #182164 on GenesisL1: 3D…
- PDB
- 7MIR
- Type
- protein
- Length
- 1,603 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-dependent glutamylase sidj; Calmodulin-2; UBIQUITINATING/DEUBIQUITINATING…
- EC
- 6.-.-.-, 3.4.22.-, 2.3.2.-, 2.4.2.31
- UniProt
- Q5ZTK6, P0DP24, Q5ZTK4
- Ligands
- AMP, ATP, MG, CA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 3 distinct chains · 53% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-dependent glutamylase sidj (EC 6.-.-.-) | protein | 750 | 53% helix, 11% strand | Q5ZTK6 |
| B | Calmodulin-2 | protein | 129 | 60% helix, 6% strand | P0DP24 |
| C | UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-, 2.3.2.-, 2.4.2.31) | protein | 724 | 52% helix, 10% strand | Q5ZTK4 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, C
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 447 | 0.83 | 0.90 | 64 | AMP |
| 2 | 327 | 0.81 | 0.91 | 47 | empty |
| 3 | 565 | 0.78 | 0.84 | 63 | empty |
| 4 | 281 | 0.77 | 0.89 | 34 | empty |
| 5 | 181 | 0.72 | 0.89 | 32 | empty |
Interfaces
2 interfaces between chains.
- A–C · 2446 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2099 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7MIR · Cryo-EM structure of SidJ-SdeA-CaM reaction intermediate complex · 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 A 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 C 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 0.43
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 Q5ZTK6
- Every structure of UniProt P0DP24
- Every structure of UniProt Q5ZTK4
- Elsewhere: RCSB PDB 7MIR · PDBe 7MIR · UniProt Q5ZTK6 · UniProt P0DP24 · UniProt Q5ZTK4
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