Research workbench
SIAH1 bound to synthetic peptide (ACE)KLRPVAMVRP(PRK)VR
Analyse SIAH1 bound to synthetic peptide (ACE)KLRPVAMVRP(PRK)VR in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I7D
- Type
- protein
- Length
- 402 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase SIAH1; Protein phyllopod
- EC
- 6.3.2.-
- UniProt
- Q8IUQ4, Q27934
- Ligands
- ACE, ZN
- Pockets
- 4 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase SIAH1 (EC 6.3.2.-) | protein | 187 | 22% helix, 42% strand | Q8IUQ4 |
| B, D | Protein phyllopod | protein | 13 | 0% helix, 46% strand | Q27934 |
| C | E3 ubiquitin-protein ligase SIAH1 (EC 6.3.2.-) | protein | 189 | 20% helix, 42% strand | Q8IUQ4 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, D
- ZN · Zinc ion · metal · 4 copies · chains A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A, C
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 | 107 | 0.38 | 0.76 | 23 | empty |
| 2 | 78 | 0.38 | 0.78 | 17 | empty |
| 3 | 79 | 0.37 | 0.78 | 17 | empty |
| 4 | 92 | 0.34 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 986 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 975 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 909 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4I7D · Siah1 bound to synthetic peptide (ACE)KLRPVAMVRP(PRK)VR · the same entry in another collection · chain A against A, 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 A against A, TM-score 0.96
- Q27934 · AlphaFold monomer V2.0 prediction for protein phyllopod (Q27934) · a predicted model of the same protein · chain B against A, TM-score 0.42
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 Q27934
- Elsewhere: RCSB PDB 4I7D · PDBe 4I7D · UniProt Q8IUQ4 · UniProt Q27934
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