MolNFT v1 · #14468 · protein
Crystal structure of the complex of human vitamin D binding protein and rabbit muscle actin
1MA9 · Vitamin D-binding protein: “Crystal structure of the complex of human vitamin D binding protein and rabbit muscle actin”. X-ray diffraction, 2 ligands (ATP, MG), 13 pockets (best druggability 0.80). MolNFT v1 #14468 on GenesisL1: 3D…
- PDB
- 1MA9
- Type
- protein
- Length
- 799 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, MG
- Pockets
- 13 · best druggability 0.80
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 | 442 | 68% helix, 0% strand | P02774 |
| B | Actin, alpha skeletal muscle | protein | 357 | 44% helix, 19% strand | P68135 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.80 | 0.85 | 50 | empty |
| 2 | 102 | 0.78 | 0.98 | 17 | empty |
| 3 | 97 | 0.75 | 0.96 | 21 | empty |
| 4 | 402 | 0.72 | 0.83 | 53 | MG, ATP |
| 5 | 529 | 0.69 | 0.78 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 1900 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 modified (disulfide, methylation).
Compared structures
- 1MA9 · Crystal structure of the complex of human vitamin D binding protein and rabbit muscle… · 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 1MA9 · PDBe 1MA9 · UniProt P02774 · UniProt P68135
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