Research workbench
Crystal structure of light MUTANT2 and DCR3 complex
Analyse Crystal structure of light MUTANT2 and DCR3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KGG
- Type
- protein
- Length
- 608 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor superfamily member 6B; Tumor necrosis factor ligand…
- UniProt
- O95407, O43557
- Ligands
- NAG, BMA, MAN, MG
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 1% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Tumor necrosis factor receptor superfamily member 6B | protein | 165 | 0% helix, 39% strand | O95407 |
| D | Tumor necrosis factor receptor superfamily member 6B | protein | 163 | 2% helix, 42% strand | O95407 |
| A | Tumor necrosis factor ligand superfamily member 14 | protein | 141 | 2% helix, 54% strand | O43557 |
| B | Tumor necrosis factor ligand superfamily member 14 | protein | 139 | 2% helix, 55% strand | O43557 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains C, D, B
- BMA · beta-D-mannopyranose · sugar · chains D
- MAN · alpha-D-mannopyranose · sugar · chains D
- MG · Magnesium ion · metal · 2 copies · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1186 | 0.79 | 0.81 | 119 | empty |
| 2 | 130 | 0.51 | 0.80 | 29 | empty |
| 3 | 91 | 0.51 | 0.83 | 24 | empty |
| 4 | 64 | 0.34 | 0.77 | 18 | empty |
| 5 | 58 | 0.33 | 0.77 | 18 | empty |
Interfaces
5 interfaces between chains.
- D–A · 619 Ų buried · 6 hydrogen bonds · protein-protein
- C–B · 595 Ų buried · 6 hydrogen bonds · protein-protein
- D–B · 561 Ų buried · 6 hydrogen bonds · protein-protein
- C–A · 557 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 467 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4KGG · Crystal structure of light mutant2 and dcr3 complex · the same entry in another collection · chain B against B, 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 B against A, TM-score 0.98
- O95407 · 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 0.96
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 O95407
- Every structure of UniProt O43557
- Elsewhere: RCSB PDB 4KGG · PDBe 4KGG · UniProt O95407 · UniProt O43557
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