Research workbench
Crystal structure of chicken CD1-1
Analyse Crystal structure of chicken CD1-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JVG
- Type
- protein
- Length
- 727 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- T-cell surface glycoprotein CD1A1 antigen; Beta-2-microglobulin
- UniProt
- A5HUM9, P21611
- Ligands
- UNL, NAG, CL
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | T-cell surface glycoprotein CD1A1 antigen | protein | 264 | 27% helix, 44% strand | A5HUM9 |
| B | T-cell surface glycoprotein CD1A1 antigen | protein | 267 | 28% helix, 43% strand | A5HUM9 |
| C, D | Beta-2-microglobulin | protein | 98 | 0% helix, 50% strand | P21611 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 595 | 0.84 | 0.88 | 55 | UNL |
| 2 | 630 | 0.83 | 0.87 | 56 | UNL |
| 3 | 786 | 0.74 | 0.79 | 65 | empty |
| 4 | 480 | 0.66 | 0.78 | 49 | empty |
| 5 | 355 | 0.65 | 0.80 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1344 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1334 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 278 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 145 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 77 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
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 A5HUM9
- Every structure of UniProt P21611
- Elsewhere: RCSB PDB 3JVG · PDBe 3JVG · UniProt A5HUM9 · UniProt P21611
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