MolNFT v1 · #163531 · protein
Legionella pneumophila sidj-human calmodulin complex
6S5T: “Legionella pneumophila sidj-human calmodulin complex”. Electron microscopy, 1 ligand (ANP), 12 pockets (best druggability 0.73). MolNFT v1 #163531 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6S5T
- Type
- protein
- Length
- 896 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sidj; Calmodulin-2
- UniProt
- Q5ZTK6, P0DP24
- Ligands
- ANP
- Pockets
- 12 · best druggability 0.73
Structure
electron microscopy · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sidj | protein | 752 | 50% helix, 11% strand | Q5ZTK6 |
| B | Calmodulin-2 | protein | 144 | 56% helix, 6% strand | P0DP24 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.73 | 0.87 | 32 | empty |
| 2 | 293 | 0.69 | 0.84 | 41 | empty |
| 3 | 420 | 0.67 | 0.80 | 45 | empty |
| 4 | 398 | 0.62 | 0.77 | 42 | empty |
| 5 | 278 | 0.60 | 0.79 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 1939 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6S5T · Legionella pneumophila SidJ-Human calmodulin 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 0.38
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
- Elsewhere: RCSB PDB 6S5T · PDBe 6S5T · UniProt Q5ZTK6 · UniProt P0DP24
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