Research workbench
Crystal structure of Se-labelled SidJ complex with CaM at 2.95 A
Analyse Crystal structure of Se-labelled SidJ complex with CaM at 2.95 A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K4L
- Type
- protein
- Length
- 1,656 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.949
- Source
- Homo sapiens; Legionella pneumophila subsp. pneumophila str. Philadelphia 1
- Molecule
- SidJ; Calmodulin-1
- UniProt
- Q5ZTK6, P0DP23
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.949 · 4 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SidJ | protein | 728 | 53% helix, 11% strand | Q5ZTK6 |
| B | SidJ | protein | 736 | 51% helix, 9% strand | Q5ZTK6 |
| C | Calmodulin-1 | protein | 111 | 48% helix, 5% strand | P0DP23 |
| D | Calmodulin-1 | protein | 81 | 43% helix, 0% strand | P0DP23 |
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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.79 | 0.90 | 36 | empty |
| 2 | 708 | 0.78 | 0.83 | 75 | CL |
| 3 | 263 | 0.72 | 0.86 | 33 | empty |
| 4 | 607 | 0.65 | 0.76 | 63 | empty |
| 5 | 222 | 0.65 | 0.84 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1431 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1197 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1030 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 6K4L · Crystal structure of se-labelled sidj complex with cam at 2.95 a · the same entry in another collection · chain D against D, 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 1.00
- P0DP23 · AlphaFold monomer V2.0 prediction for calmodulin-1 (P0DP23) · a predicted model of the same protein · chain D against A, TM-score 0.55
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 P0DP23
- Elsewhere: RCSB PDB 6K4L · PDBe 6K4L · UniProt Q5ZTK6 · UniProt P0DP23
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