Research workbench
Crystal structure of the complex of actin with vitamin D-binding protein
Analyse Crystal structure of the complex of actin with vitamin D-binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LOT
- Type
- protein
- Length
- 796 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin D-binding protein; Actin, alpha skeletal muscle
- UniProt
- P02774, P68135
- Ligands
- ATP, CA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin D-binding protein | protein | 436 | 70% helix, 0% strand | P02774 |
| B | Actin, alpha skeletal muscle | protein | 360 | 41% helix, 19% strand | P68135 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains B
- CA · Calcium ion · metal · chains B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.78 | 0.98 | 20 | empty |
| 2 | 102 | 0.77 | 0.97 | 16 | empty |
| 3 | 484 | 0.77 | 0.84 | 68 | GOL |
| 4 | 424 | 0.74 | 0.84 | 54 | CA, ATP |
| 5 | 170 | 0.66 | 0.86 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1893 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 1 modified (disulfide, methylation).
Compared structures
- 1LOT · Crystal structure of the complex of actin with vitamin D-binding protein · the same entry in another collection · chain A against A, TM-score 1.00
- P02774 · AlphaFold monomer V2.0 prediction for vitamin D-binding protein (P02774) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P02774
- Every structure of UniProt P68135
- Elsewhere: RCSB PDB 1LOT · PDBe 1LOT · UniProt P02774 · UniProt P68135
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