Research workbench
Crystal structure of mouse DCAR2 crd domain complex with IPM2
Analyse Crystal structure of mouse DCAR2 crd domain complex with IPM2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LFJ
- Type
- protein
- Length
- 265 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-type lectin domain family 4, member B1
- UniProt
- Q9D8Q7
- Ligands
- IPD, MAN, CA
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-type lectin domain family 4, member B1 | protein | 133 | 17% helix, 32% strand | Q9D8Q7 |
| B | C-type lectin domain family 4, member B1 | protein | 132 | 17% helix, 32% strand | Q9D8Q7 |
Ligands and binding sites
- IPD · D-myo-inositol-1-phosphate · ligand · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.64 | 0.83 | 34 | empty |
| 2 | 142 | 0.44 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 578 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6LFJ · Crystal structure of mouse DCAR2 CRD domain complex with IPM2 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q9D8Q7
- Elsewhere: RCSB PDB 6LFJ · PDBe 6LFJ · UniProt Q9D8Q7
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