MolNFT v1 · #117141 · protein
Crystal structure of WW4 domain of itch in complex with txnip peptide
5DZD · E3 ubiquitin-protein ligase itchy homolog: “Crystal structure of WW4 domain of itch in complex with txnip peptide”. X-ray diffraction, 3 ligands (ACE, UNX, NH2). MolNFT v1 #117141 on GenesisL1: 3D structure, binding sites and…
- 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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