Research workbench
Legionella pneumophila sidj/ calmodulin 2 complex
Analyse Legionella pneumophila sidj/ calmodulin 2 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PLM
- Type
- protein
- Length
- 1,779 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sidj protein; Calmodulin-2
- UniProt
- Q5ZTK6, P0DP24
- Ligands
- POP, AMP, CA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sidj protein | protein | 748 | 54% helix, 12% strand | Q5ZTK6 |
| B | Sidj protein | protein | 752 | 53% helix, 13% strand | Q5ZTK6 |
| C | Calmodulin-2 | protein | 134 | 62% helix, 6% strand | P0DP24 |
| D | Calmodulin-2 | protein | 145 | 59% helix, 8% strand | P0DP24 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.84 | 0.85 | 113 | empty |
| 2 | 491 | 0.76 | 0.84 | 57 | empty |
| 3 | 230 | 0.74 | 0.89 | 38 | empty |
| 4 | 437 | 0.73 | 0.83 | 48 | empty |
| 5 | 65 | 0.72 | 0.97 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–D · 2392 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2270 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1216 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- Q5ZTK6 · AlphaFold monomer V2.0 prediction for calmodulin-dependent glutamylase sidj (Q5ZTK6) · a predicted model of the same protein · chain B against A, TM-score 1.00
- P0DP24 · AlphaFold monomer V2.0 prediction for calmodulin-2 (P0DP24) · a predicted model of the same protein · chain C 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 Q5ZTK6
- Every structure of UniProt P0DP24
- Elsewhere: RCSB PDB 6PLM · PDBe 6PLM · UniProt Q5ZTK6 · UniProt P0DP24
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