Research workbench
The crystal structure of the msp domain of human MOSPD2 in complex with the phospho-ffat motif of STARD3.
Analyse The crystal structure of the msp domain of human MOSPD2 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TQU
- Type
- protein
- Length
- 268 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Motile sperm domain-containing protein 2; Star-related lipid transfer protein 3
- UniProt
- Q8NHP6, Q14849
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Motile sperm domain-containing protein 2 | protein | 124 | 10% helix, 46% strand | Q8NHP6 |
| B | Motile sperm domain-containing protein 2 | protein | 123 | 11% helix, 46% strand | Q8NHP6 |
| C | Star-related lipid transfer protein 3 | protein | 10 | 0% helix, 10% strand | Q14849 |
| D | Star-related lipid transfer protein 3 | protein | 11 | 0% helix, 9% strand | Q14849 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.46 | 0.77 | 24 | empty |
| 2 | 75 | 0.35 | 0.76 | 16 | empty |
| 3 | 52 | 0.28 | 0.75 | 16 | empty |
| 4 | 50 | 0.28 | 0.75 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 808 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 713 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 543 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 68 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (phosphorylation).
Compared structures
- 6TQU · The crystal structure of the MSP domain of human MOSPD2 in complex with the Phospho-FFAT… · the same entry in another collection · chain D against D, TM-score 1.00
- Q8NHP6 · AlphaFold monomer V2.0 prediction for motile sperm domain-containing protein 2 (Q8NHP6) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q14849 · AlphaFold monomer V2.0 prediction for star-related lipid transfer protein 3 (Q14849) · a predicted model of the same protein · chain C against A, TM-score 0.41
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 Q8NHP6
- Every structure of UniProt Q14849
- Elsewhere: RCSB PDB 6TQU · PDBe 6TQU · UniProt Q8NHP6 · UniProt Q14849
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