Research workbench
Crystal structure of sumo E1 in complex with an allosteric inhibitor
Analyse Crystal structure of sumo E1 in complex with an allosteric inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CWY
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sumo-activating enzyme subunit 1; Sumo-activating enzyme subunit 2
- EC
- 2.3.2.-
- UniProt
- Q9UBE0, Q9UBT2
- Ligands
- FHJ, ZN, MG, SO4
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Sumo-activating enzyme subunit 1 | protein | 304 | 45% helix, 21% strand | Q9UBE0 |
| D | Sumo-activating enzyme subunit 2 (EC 2.3.2.-) | protein | 487 | 37% helix, 17% strand | Q9UBT2 |
Ligands and binding sites
- FHJ · dimethyl (1S,2S,3R,4R)-1-[(1S)-2-(4-methylphenyl)-1-(phenylamino)ethyl]-7-oxabicyclo[2.2.1]hept-5-ene-2,3-dicarboxylate · ligand · chains C, D
- ZN · Zinc ion · metal · chains D
- MG · Magnesium ion · metal · chains D
- SO4 · Sulfate ion · ion · 4 copies · chains D
- GOL · Glycerol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.83 | 0.84 | 114 | SO4, FHJ |
| 2 | 609 | 0.75 | 0.81 | 79 | GOL |
| 3 | 242 | 0.57 | 0.78 | 32 | empty |
| 4 | 119 | 0.44 | 0.77 | 18 | GOL |
| 5 | 127 | 0.42 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- C–D · 2298 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6CWY · Crystal structure of SUMO E1 in complex with an allosteric inhibitor · the same entry in another collection · chain C against C, TM-score 1.00
- Q9UBE0 · AlphaFold monomer V2.0 prediction for sumo-activating enzyme subunit 1 (Q9UBE0) · a predicted model of the same protein · chain C against A, TM-score 0.95
- Q9UBT2 · AlphaFold monomer V2.0 prediction for sumo-activating enzyme subunit 2 (Q9UBT2) · a predicted model of the same protein · chain D against A, TM-score 0.70
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 Q9UBE0
- Every structure of UniProt Q9UBT2
- Elsewhere: RCSB PDB 6CWY · PDBe 6CWY · UniProt Q9UBE0 · UniProt Q9UBT2
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