MolNFT v1 · #3694 · protein
Crystal structure of death receptor 5 (DR5) bound to APO2L/TRAIL
1D0G · Death receptor-5: “Crystal structure of death receptor 5 (DR5) bound to APO2L/TRAIL”. X-ray diffraction, 2 ligands (ZN, CL), 13 pockets (best druggability 0.79). MolNFT v1 #3694 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1D0G
- Type
- protein
- Length
- 781 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death receptor-5; Apoptosis-2 ligand
- UniProt
- O14763, P50591
- Ligands
- ZN, CL
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 1% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Death receptor-5 | protein | 108 | 0% helix, 40% strand | O14763 |
| S, T | Death receptor-5 | protein | 110 | 0% helix, 41% strand | O14763 |
| A, B, D | Apoptosis-2 ligand | protein | 151 | 2% helix, 52% strand | P50591 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.79 | 0.99 | 23 | empty |
| 2 | 942 | 0.76 | 0.79 | 74 | empty |
| 3 | 714 | 0.72 | 0.78 | 59 | empty |
| 4 | 577 | 0.71 | 0.79 | 49 | empty |
| 5 | 195 | 0.61 | 0.82 | 22 | empty |
Interfaces
9 interfaces between chains.
- A–D · 1382 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1310 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 1277 Ų buried · 22 hydrogen bonds · protein-protein
- S–A · 942 Ų buried · 20 hydrogen bonds · protein-protein
- R–D · 927 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide (disulfide).
Compared structures
- 1D0G · Crystal structure of death receptor 5 (DR5) bound to APO2L/TRAIL · the same entry in another collection · chain D against D, 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 0.97
- O14763 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain R 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 O14763
- Every structure of UniProt P50591
- Elsewhere: RCSB PDB 1D0G · PDBe 1D0G · UniProt O14763 · UniProt P50591
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