Research workbench
Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to trail (TNFSF10)
Analyse Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to trail (TNFSF10) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CIR
- Type
- protein
- Length
- 752 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor ligand superfamily member 10; Tumor necrosis factor receptor…
- UniProt
- P50591, O00220
- Ligands
- ZN, CL
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 6 distinct chains · 1% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor ligand superfamily member 10 | protein | 149 | 2% helix, 54% strand | P50591 |
| B | Tumor necrosis factor ligand superfamily member 10 | protein | 151 | 2% helix, 54% strand | P50591 |
| D | Tumor necrosis factor ligand superfamily member 10 | protein | 150 | 2% helix, 54% strand | P50591 |
| E | Tumor necrosis factor receptor superfamily member 10A | protein | 102 | 0% helix, 33% strand | O00220 |
| F | Tumor necrosis factor receptor superfamily member 10A | protein | 98 | 0% helix, 35% strand | O00220 |
| G | Tumor necrosis factor receptor superfamily member 10A | protein | 102 | 0% helix, 30% strand | O00220 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 117 | 0.79 | 0.98 | 24 | empty |
| 2 | 532 | 0.69 | 0.79 | 47 | empty |
| 3 | 521 | 0.69 | 0.79 | 46 | empty |
| 4 | 514 | 0.68 | 0.79 | 48 | empty |
| 5 | 63 | 0.58 | 0.89 | 19 | empty |
Interfaces
9 interfaces between chains.
- B–D · 1275 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1270 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1239 Ų buried · 16 hydrogen bonds · protein-protein
- D–G · 835 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 762 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 5CIR · Crystal structure of death receptor 4 (DR4; TNFFRSF10A) bound to TRAIL (TNFSF10) · the same entry in another collection · chain G against G, TM-score 1.00
- P50591 · AlphaFold monomer V2.0 prediction for tumor necrosis factor ligand superfamily member 10… · a predicted model of the same protein · chain A against A, TM-score 0.98
- O00220 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain F 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 P50591
- Every structure of UniProt O00220
- Elsewhere: RCSB PDB 5CIR · PDBe 5CIR · UniProt P50591 · UniProt O00220
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