Research workbench
Crystal structure of HERC2 zz domain in complex with SUMO1 tail
Analyse Crystal structure of HERC2 zz domain in complex with SUMO1 tail in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WW3
- Type
- protein
- Length
- 118 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SUMO1 linked HERC2 zz domain (small ubiquitin-related modifier 1,E3 ubiquitin-protein…
- EC
- 2.3.2.26
- UniProt
- P63165, O95714
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SUMO1 linked HERC2 zz domain (small ubiquitin-related modifier 1,E3 ubiquitin-protein ligase HERC2) (EC 2.3.2.26) | protein | 60 | 15% helix, 23% strand | P63165, O95714 |
| B | SUMO1 linked HERC2 zz domain (small ubiquitin-related modifier 1,E3 ubiquitin-protein ligase HERC2) (EC 2.3.2.26) | protein | 58 | 16% helix, 24% strand | P63165, O95714 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
- GOL · Glycerol · additive · chains B
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 | 0.33 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 237 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6WW3 · Crystal structure of HERC2 ZZ domain in complex with SUMO1 tail · the same entry in another collection · chain A against A, TM-score 1.00
- P63165 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 1 (P63165) · a predicted model of the same protein · chain B against A, TM-score 0.35
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 P63165
- Every structure of UniProt O95714
- Elsewhere: RCSB PDB 6WW3 · PDBe 6WW3 · UniProt P63165 · UniProt O95714
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