Research workbench
Crystal structure of sidj-cam-AMP ternary complex at 3.11 a
Analyse Crystal structure of sidj-cam-AMP ternary complex at 3.11 a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6K4R
- Type
- protein
- Length
- 1,667 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sidj; Calmodulin-1
- UniProt
- Q5ZTK6, P0DP23
- Ligands
- AMP, CA, CL
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sidj | protein | 731 | 51% helix, 11% strand | Q5ZTK6 |
| B | Sidj | protein | 738 | 51% helix, 10% strand | Q5ZTK6 |
| C | Calmodulin-1 | protein | 116 | 45% helix, 3% strand | P0DP23 |
| D | Calmodulin-1 | protein | 82 | 41% helix, 0% strand | P0DP23 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains C, D
- CL · Chloride ion · ion · 4 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B, 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 | 630 | 0.76 | 0.82 | 64 | CL |
| 2 | 324 | 0.76 | 0.88 | 33 | empty |
| 3 | 242 | 0.71 | 0.86 | 33 | empty |
| 4 | 733 | 0.70 | 0.77 | 72 | CL |
| 5 | 296 | 0.68 | 0.83 | 33 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1488 Ų buried · 19 hydrogen bonds · protein-protein
- B–D · 1236 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1055 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6K4R · Crystal structure of SidJ-CaM-AMP ternary complex at 3.11 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 6K4R · PDBe 6K4R · UniProt Q5ZTK6 · UniProt P0DP23
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