Research workbench
Crystal structure of SIAH1 sina domain in complex with a USP19 peptide
Analyse Crystal structure of SIAH1 sina domain in complex with a USP19 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X3G
- Type
- protein
- Length
- 399 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase SIAH1; Ubiquitin carboxyl-terminal hydrolase 19
- EC
- 6.3.2.-, 3.4.19.12
- UniProt
- Q8IUQ4, O94966
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase SIAH1 (EC 6.3.2.-) | protein | 188 | 20% helix, 43% strand | Q8IUQ4 |
| B | E3 ubiquitin-protein ligase SIAH1 (EC 6.3.2.-) | protein | 190 | 18% helix, 43% strand | Q8IUQ4 |
| C | Ubiquitin carboxyl-terminal hydrolase 19 (EC 3.4.19.12) | protein | 11 | 0% helix, 36% strand | O94966 |
| D | Ubiquitin carboxyl-terminal hydrolase 19 (EC 3.4.19.12) | protein | 10 | 0% helix, 50% strand | O94966 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.46 | 0.75 | 28 | empty |
| 2 | 98 | 0.35 | 0.74 | 18 | empty |
| 3 | 93 | 0.35 | 0.75 | 20 | empty |
| 4 | 80 | 0.34 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1021 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 669 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 643 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4X3G · Crystal structure of SIAH1 SINA domain in complex with a USP19 peptide · the same entry in another collection · chain D against D, TM-score 1.00
- Q8IUQ4 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase SIAH1 (Q8IUQ4) · a predicted model of the same protein · chain B against A, TM-score 0.97
- O94966 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase 19 (O94966) · a predicted model of the same protein · chain D against A, TM-score 0.54
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 Q8IUQ4
- Every structure of UniProt O94966
- Elsewhere: RCSB PDB 4X3G · PDBe 4X3G · UniProt Q8IUQ4 · UniProt O94966
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