Research workbench
Crystal structure of sidj-cam binary complex at 2.71 a
Analyse Crystal structure of sidj-cam binary complex at 2.71 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K4K
- Type
- protein
- Length
- 1,686 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sidj; Calmodulin-1
- UniProt
- Q5ZTK6, P0DP23
- Ligands
- CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sidj | protein | 734 | 52% helix, 10% strand | Q5ZTK6 |
| B | Sidj | protein | 737 | 52% helix, 10% strand | Q5ZTK6 |
| C | Calmodulin-1 | protein | 120 | 41% helix, 0% strand | P0DP23 |
| D | Calmodulin-1 | protein | 95 | 40% helix, 0% strand | P0DP23 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.79 | 0.83 | 74 | empty |
| 2 | 335 | 0.76 | 0.87 | 35 | empty |
| 3 | 311 | 0.76 | 0.88 | 34 | empty |
| 4 | 805 | 0.72 | 0.78 | 68 | empty |
| 5 | 440 | 0.66 | 0.79 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1772 Ų buried · 23 hydrogen bonds · protein-protein
- B–D · 1558 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1058 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6K4K · Crystal structure of SidJ-CaM binary complex at 2.71 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 0.49
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 6K4K · PDBe 6K4K · UniProt Q5ZTK6 · UniProt P0DP23
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