MolNFT v1 · #94797 · protein
SIAH1 mutant bound to synthetic peptide (ACE)KLRPV(23P)MVRPWVR
4I7C · E3 ubiquitin-protein ligase SIAH1: “SIAH1 mutant bound to synthetic peptide (ACE)KLRPV(23P)MVRPWVR”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.40). MolNFT v1 #94797 on GenesisL1: 3D structure, binding sites…
- PDB
- 4I7C
- Type
- protein
- Length
- 404 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
- ZN
- Pockets
- 7 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase SIAH1 (EC 6.3.2.-) | protein | 188 | 21% helix, 41% strand | Q8IUQ4 |
| B, D | Protein phyllopod | protein | 13 | 0% helix, 46% strand | Q27934 |
| C | E3 ubiquitin-protein ligase SIAH1 (EC 6.3.2.-) | protein | 190 | 22% helix, 42% strand | Q8IUQ4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.40 | 0.78 | 21 | MPD |
| 2 | 64 | 0.39 | 0.80 | 21 | empty |
| 3 | 61 | 0.38 | 0.80 | 18 | empty |
| 4 | 79 | 0.36 | 0.77 | 16 | empty |
| 5 | 76 | 0.36 | 0.76 | 13 | MPD |
Interfaces
3 interfaces between chains.
- A–C · 1034 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 920 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 886 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4I7C · Siah1 mutant bound to synthetic peptide (ACE)KLRPV(23P)MVRPWVR · 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 C against A, TM-score 0.97
- Q27934 · AlphaFold monomer V2.0 prediction for protein phyllopod (Q27934) · a predicted model of the same protein · chain B against A, TM-score 0.36
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 4I7C · PDBe 4I7C · UniProt Q8IUQ4 · UniProt Q27934
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