Research workbench
Cryo-EM structure of sidj-sdec-cam reaction intermediate complex
Analyse Cryo-EM structure of sidj-sdec-cam reaction intermediate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MIS
- Type
- protein
- Length
- 1,616 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin-dependent glutamylase sidj; Calmodulin; Sdec
- EC
- 6.-.-.-
- UniProt
- Q5ZTK6, P0DP24, Q6RCQ8
- Ligands
- ATP, AMP, MG, NA, CA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 52% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin-dependent glutamylase sidj (EC 6.-.-.-) | protein | 749 | 53% helix, 11% strand | Q5ZTK6 |
| B | Calmodulin | protein | 133 | 56% helix, 5% strand | P0DP24 |
| C | Sdec | protein | 734 | 51% helix, 9% strand | Q6RCQ8 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- AMP · Adenosine monophosphate · ligand · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 693 | 0.87 | 0.91 | 84 | NA, AMP |
| 2 | 468 | 0.76 | 0.84 | 59 | empty |
| 3 | 147 | 0.76 | 0.93 | 23 | empty |
| 4 | 652 | 0.74 | 0.80 | 65 | empty |
| 5 | 134 | 0.73 | 0.92 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1884 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1829 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7MIS · Cryo-EM structure of SidJ-SdeC-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
- P0DP24 · AlphaFold monomer V2.0 prediction for calmodulin-2 (P0DP24) · a predicted model of the same protein · chain B against A, TM-score 0.42
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 Q6RCQ8
- Elsewhere: RCSB PDB 7MIS · PDBe 7MIS · UniProt Q5ZTK6 · UniProt P0DP24 · UniProt Q6RCQ8
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