Research workbench
Structure of TNF receptor associated factor 2 in complex with a human CD30 peptide
Analyse Structure of TNF receptor associated factor 2 in complex with a human CD30… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D01
- Type
- protein
- Length
- 1,032 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor associated factor 2; CD30 peptide
- UniProt
- Q12933, P28908
- Ligands
- ACE
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Tumor necrosis factor receptor associated factor 2 | protein | 168 | 18% helix, 31% strand | Q12933 |
| G, H, I | CD30 peptide | protein | 8 | 0% helix, 38% strand | P28908 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains D, G, E, H, F, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 932 | 0.74 | 0.78 | 73 | empty |
| 2 | 784 | 0.72 | 0.78 | 58 | empty |
| 3 | 213 | 0.52 | 0.77 | 20 | empty |
| 4 | 121 | 0.38 | 0.73 | 23 | empty |
| 5 | 108 | 0.37 | 0.74 | 23 | empty |
Interfaces
11 interfaces between chains.
- E–H · 580 Ų buried · 15 hydrogen bonds · protein-protein
- F–I · 576 Ų buried · 15 hydrogen bonds · protein-protein
- D–G · 571 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 569 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 569 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1D01 · Structure of TNF receptor associated factor 2 in complex with a human CD30 peptide · the same entry in another collection · chain I against I, TM-score 1.00
- Q12933 · AlphaFold monomer V2.0 prediction for TNF receptor-associated factor 2 (Q12933) · a predicted model of the same protein · chain A against A, TM-score 0.97
- P28908 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member 8… · a predicted model of the same protein · chain G against A, TM-score 0.50
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 Q12933
- Every structure of UniProt P28908
- Elsewhere: RCSB PDB 1D01 · PDBe 1D01 · UniProt Q12933 · UniProt P28908
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