Research workbench
Solution of the variably-twinned structure of a novel calmodulin- peptide complex in a novel configuration
Analyse Solution of the variably-twinned structure of a novel calmodulin- peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DOW
- Type
- protein
- Length
- 667 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin; Chloride anion exchanger
- UniProt
- P62158, Q9WVC8
- Ligands
- CA, NA, CL, NH2, SO4
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin | protein | 148 | 57% helix, 6% strand | P62158 |
| B | Chloride anion exchanger | protein | 19 | 79% helix, 0% strand | Q9WVC8 |
| C, G | Calmodulin | protein | 146 | 60% helix, 5% strand | P62158 |
| D | Chloride anion exchanger | protein | 21 | 67% helix, 0% strand | Q9WVC8 |
| E | Calmodulin | protein | 147 | 60% helix, 4% strand | P62158 |
| F, H | Chloride anion exchanger | protein | 20 | 75% helix, 0% strand | Q9WVC8 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, C, E, G
- NA · Sodium ion · metal · 5 copies · chains A, C, G
- CL · Chloride ion · ion · 11 copies · chains A, C, E, F, G, H
- NH2 · Amino group · ion · 4 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.85 | 0.86 | 87 | NA |
| 2 | 296 | 0.66 | 0.82 | 32 | NH2 |
| 3 | 363 | 0.57 | 0.75 | 34 | CL |
| 4 | 215 | 0.52 | 0.76 | 29 | empty |
| 5 | 112 | 0.48 | 0.80 | 17 | empty |
Interfaces
10 interfaces between chains.
- E–F · 1347 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1327 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1302 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1215 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 574 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5DOW · Solution of the Variably-Twinned Structure of a Novel Calmodulin-Peptide Complex in a… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9WVC8 · AlphaFold monomer V2.0 prediction for chloride anion exchanger (Q9WVC8) · a predicted model of the same protein · chain B against A, TM-score 0.58
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 P62158
- Every structure of UniProt Q9WVC8
- Elsewhere: RCSB PDB 5DOW · PDBe 5DOW · UniProt P62158 · UniProt Q9WVC8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.