Research workbench
The crystal structure of light in complex with hvem and CD160
Analyse The crystal structure of light in complex with hvem and CD160 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MSG
- Type
- protein
- Length
- 1,044 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 14, membrane form; CD160 antigen, soluble…
- UniProt
- O43557, O95971, Q92956
- Ligands
- NAG, BMA
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Tumor necrosis factor ligand superfamily member 14, membrane form | protein | 142 | 2% helix, 56% strand | O43557 |
| D, E, F | CD160 antigen, soluble FORM,TUMOR necrosis factor receptor superfamily member 14 | protein | 206 | 4% helix, 50% strand | O95971, Q92956 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains D, E, F
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 668 | 0.76 | 0.82 | 78 | empty |
| 2 | 494 | 0.71 | 0.81 | 56 | empty |
| 3 | 395 | 0.69 | 0.81 | 55 | empty |
| 4 | 323 | 0.69 | 0.83 | 47 | empty |
| 5 | 83 | 0.67 | 0.92 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–C · 956 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 955 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 953 Ų buried · 20 hydrogen bonds · protein-protein
- A–F · 743 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 736 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7MSG · The crystal structure of LIGHT in complex with HVEM and CD160 · the same entry in another collection · chain F against F, TM-score 1.00
- O43557 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 14… · a predicted model of the same protein · chain A against A, TM-score 0.97
- O95971 · AlphaFold monomer V2.0 prediction for CD160 antigen (O95971) · a predicted model of the same protein · chain F against A, TM-score 0.50
- Q92956 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain D against A, TM-score 0.48
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 O43557
- Every structure of UniProt O95971
- Every structure of UniProt Q92956
- Elsewhere: RCSB PDB 7MSG · PDBe 7MSG · UniProt O43557 · UniProt O95971 · UniProt Q92956
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