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Crystallographic structure of the mouse sign-R1 crd domain in complex with sialic acid
Analyse Crystallographic structure of the mouse sign-R1 crd domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CAJ
- Type
- protein
- Length
- 528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD209 antigen-like protein B
- UniProt
- Q8CJ91
- Ligands
- SIA, CA, SO4, CL
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CD209 antigen-like protein B | protein | 131 | 23% helix, 34% strand | Q8CJ91 |
| B | CD209 antigen-like protein B | protein | 133 | 22% helix, 29% strand | Q8CJ91 |
| C, D | CD209 antigen-like protein B | protein | 132 | 22% helix, 30% strand | Q8CJ91 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 30 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.81 | 0.97 | 27 | empty |
| 2 | 112 | 0.79 | 0.98 | 31 | SO4 |
| 3 | 60 | 0.70 | 0.97 | 19 | SO4 |
| 4 | 165 | 0.57 | 0.81 | 29 | CL, SO4 |
| 5 | 98 | 0.35 | 0.74 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 992 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 946 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 594 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 105 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 95 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 4CAJ · Crystallographic structure of the mouse SIGN-R1 CRD domain in complex with sialic acid · the same entry in another collection · chain D against D, TM-score 1.00
- Q8CJ91 · AlphaFold monomer V2.0 prediction for CD209 antigen-like protein B (Q8CJ91) · a predicted model of the same protein · chain D 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 Q8CJ91
- Elsewhere: RCSB PDB 4CAJ · PDBe 4CAJ · UniProt Q8CJ91
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