Research workbench
Crystal structure of WW4 domain of itch in complex with txnip peptide
Analyse Crystal structure of WW4 domain of itch in complex with txnip peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DZD
- Type
- protein
- Length
- 98 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase itchy homolog; Thioredoxin-interacting protein
- EC
- 6.3.2.-
- UniProt
- Q96J02, Q9H3M7
- Ligands
- ACE, UNX, NH2
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase itchy homolog (EC 6.3.2.-) | protein | 37 | 0% helix, 41% strand | Q96J02 |
| B | E3 ubiquitin-protein ligase itchy homolog (EC 6.3.2.-) | protein | 39 | 0% helix, 33% strand | Q96J02 |
| C | Thioredoxin-interacting protein | protein | 12 | 33% helix, 0% strand | Q9H3M7 |
| D | Thioredoxin-interacting protein | protein | 10 | 40% helix, 0% strand | Q9H3M7 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains C
- UNX · Unknown atom or ion · ion · 17 copies · chains A, C, B, D
- NH2 · Amino group · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- A–C · 382 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 373 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 266 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 244 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 97 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 5DZD · Crystal Structure of WW4 domain of ITCH in complex with TXNIP peptide · the same entry in another collection · chain D against D, TM-score 1.00
- Q96J02 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase itchy homolog (Q96J02) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q9H3M7 · AlphaFold monomer V2.0 prediction for thioredoxin-interacting protein (Q9H3M7) · a predicted model of the same protein · chain D against A, TM-score 0.53
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 Q96J02
- Every structure of UniProt Q9H3M7
- Elsewhere: RCSB PDB 5DZD · PDBe 5DZD · UniProt Q96J02 · UniProt Q9H3M7
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