MolNFT v1 · #159483 · protein
Legionella pneumophila SIDJ/SACCHAROMYCES cerevisiae calmodulin complex
6OQQ: “Legionella pneumophila SIDJ/SACCHAROMYCES cerevisiae calmodulin complex”. X-ray diffraction, 5 ligands (POP, AMP, MG), 20 pockets (best druggability 0.80). MolNFT v1 #159483 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6OQQ
- Type
- protein
- Length
- 1,755 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Legionella pneumophila sidj; Calmodulin
- UniProt
- Q5ZTK6, P06787
- Ligands
- POP, AMP, MG, CA, NA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Legionella pneumophila sidj | protein | 748 | 53% helix, 12% strand | Q5ZTK6 |
| B | Calmodulin | protein | 133 | 60% helix, 6% strand | P06787 |
| C | Legionella pneumophila sidj | protein | 743 | 53% helix, 12% strand | Q5ZTK6 |
| D | Calmodulin | protein | 131 | 59% helix, 5% strand | P06787 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 3 copies · chains A, C
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 7 copies · chains A, C
- CA · Calcium ion · metal · 4 copies · chains B, D
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C
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 | 715 | 0.80 | 0.84 | 71 | EDO |
| 2 | 631 | 0.78 | 0.84 | 60 | EDO |
| 3 | 750 | 0.75 | 0.80 | 60 | EDO |
| 4 | 1009 | 0.73 | 0.76 | 71 | EDO |
| 5 | 322 | 0.69 | 0.83 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2135 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1617 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1259 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 6OQQ · Legionella pneumophila SidJ/Saccharomyces cerevisiae calmodulin complex · 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
- P06787 · AlphaFold monomer V2.0 prediction for calmodulin (P06787) · a predicted model of the same protein · chain D 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 P06787
- Elsewhere: RCSB PDB 6OQQ · PDBe 6OQQ · UniProt Q5ZTK6 · UniProt P06787
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