Research workbench
Three-dimensional structure of a complex between the death domains of pelle and tube
Analyse Three-dimensional structure of a complex between the death domains of pelle and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D2Z
- Type
- protein
- Length
- 513 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Death domain of pelle; Death domain of tube
- UniProt
- Q05652, P22812
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Death domain of pelle | protein | 102 | 73% helix, 2% strand | Q05652 |
| B | Death domain of tube | protein | 150 | 55% helix, 3% strand | P22812 |
| C | Death domain of pelle | protein | 108 | 65% helix, 3% strand | Q05652 |
| D | Death domain of tube | protein | 153 | 54% helix, 3% strand | P22812 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.56 | 0.79 | 23 | EPE |
| 2 | 166 | 0.50 | 0.78 | 18 | empty |
| 3 | 94 | 0.43 | 0.79 | 21 | empty |
| 4 | 57 | 0.34 | 0.78 | 14 | empty |
| 5 | 97 | 0.34 | 0.74 | 16 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1134 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 898 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 483 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 68 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1D2Z · Three-dimensional structure of a complex between the death domains of pelle and tube · the same entry in another collection · chain D against D, TM-score 1.00
- P22812 · AlphaFold monomer V2.0 prediction for protein tube (P22812) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q05652 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase pelle (Q05652) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q05652
- Every structure of UniProt P22812
- Elsewhere: RCSB PDB 1D2Z · PDBe 1D2Z · UniProt Q05652 · UniProt P22812
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