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Crystallographic structure of the native mouse sign-R1 crd domain
Analyse Crystallographic structure of the native mouse sign-R1 crd domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZHG
- Type
- protein
- Length
- 529 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CD209 antigen-like protein B
- UniProt
- Q8CJ91
- Ligands
- CA, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | CD209 antigen-like protein B | protein | 132 | 22% helix, 34% strand | Q8CJ91 |
| D | CD209 antigen-like protein B | protein | 133 | 18% helix, 29% strand | Q8CJ91 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D
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 | 142 | 0.81 | 0.97 | 26 | empty |
| 2 | 50 | 0.71 | 0.99 | 17 | SO4 |
| 3 | 52 | 0.69 | 0.97 | 18 | SO4 |
| 4 | 371 | 0.56 | 0.74 | 44 | empty |
| 5 | 50 | 0.39 | 0.81 | 11 | empty |
Interfaces
5 interfaces between chains.
- C–D · 975 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 956 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 641 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 176 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 96 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3ZHG · Crystallographic structure of the native mouse SIGN-R1 CRD domain · 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 3ZHG · PDBe 3ZHG · UniProt Q8CJ91
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