Research workbench
Crystal structure of yeast calmodulin bound to the C-terminal fragment of spindle pole body protein SPC110
Analyse Crystal structure of yeast calmodulin bound to the C-terminal fragment of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DS7
- Type
- protein
- Length
- 737 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin; Spindle pole body component 110
- UniProt
- O60041, P32380
- Ligands
- SR, SO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 7 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Calmodulin | protein | 144 | 63% helix, 7% strand | O60041 |
| B | Calmodulin | protein | 142 | 62% helix, 4% strand | O60041 |
| C, D | Calmodulin | protein | 143 | 62% helix, 6% strand | O60041 |
| E | Spindle pole body component 110 | protein | 46 | 72% helix, 0% strand | P32380 |
| F | Spindle pole body component 110 | protein | 39 | 90% helix, 0% strand | P32380 |
| G | Spindle pole body component 110 | protein | 36 | 92% helix, 0% strand | P32380 |
| H | Spindle pole body component 110 | protein | 44 | 75% helix, 0% strand | P32380 |
Ligands and binding sites
- SR · Strontium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains A, C
- GOL · Glycerol · additive · 4 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 698 | 0.68 | 0.76 | 59 | empty |
| 2 | 94 | 0.45 | 0.80 | 23 | empty |
| 3 | 62 | 0.27 | 0.72 | 19 | GOL |
Interfaces
11 interfaces between chains.
- C–D · 1432 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1326 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 1097 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 1071 Ų buried · 4 hydrogen bonds · protein-protein
- D–H · 1059 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4DS7 · Crystal structure of yeast calmodulin bound to the C-terminal fragment of spindle pole… · the same entry in another collection · chain H against H, TM-score 1.00
- P32380 · AlphaFold monomer V2.0 prediction for spindle pole body component 110 (P32380) · a predicted model of the same protein · chain F against A, TM-score 0.90
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 O60041
- Every structure of UniProt P32380
- Elsewhere: RCSB PDB 4DS7 · PDBe 4DS7 · UniProt O60041 · UniProt P32380
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