Research workbench
Crystal structure of itch WW3 domain in complex with txnip peptide
Analyse Crystal structure of itch WW3 domain 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
- 5DWS
- Type
- protein
- Length
- 190 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase itchy homolog; Txnip
- EC
- 6.3.2.-
- UniProt
- Q96J02
- Ligands
- UNX, NH2
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 5 distinct chains · 13% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | E3 ubiquitin-protein ligase itchy homolog (EC 6.3.2.-) | protein | 37 | 8% helix, 35% strand | Q96J02 |
| B, D, F | Txnip | protein | 10 | 40% helix, 0% strand | — |
| C | E3 ubiquitin-protein ligase itchy homolog (EC 6.3.2.-) | protein | 40 | 8% helix, 33% strand | Q96J02 |
| E | E3 ubiquitin-protein ligase itchy homolog (EC 6.3.2.-) | protein | 35 | 9% helix, 37% strand | Q96J02 |
| H | Txnip | protein | 11 | 36% helix, 0% strand | — |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 26 copies · chains A, E, C, D, F, H, G
- NH2 · Amino group · ion · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.32 | 0.74 | 18 | empty |
Interfaces
8 interfaces between chains.
- E–F · 410 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 403 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 401 Ų buried · 2 hydrogen bonds · protein-protein
- G–H · 389 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 385 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5DWS · Crystal Structure of ITCH WW3 domain in complex with TXNIP peptide · the same entry in another collection · chain H against H, 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 0.91
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
- Elsewhere: RCSB PDB 5DWS · PDBe 5DWS · UniProt Q96J02
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