Research workbench
Crystal structure of apo sumo E1
Analyse Crystal structure of apo sumo E1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CWZ
- Type
- protein
- Length
- 818 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
- ZN
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Sumo-activating enzyme subunit 1 | protein | 312 | 41% helix, 20% strand | Q9UBE0 |
| D | Sumo-activating enzyme subunit 2 (EC 2.3.2.-) | protein | 506 | 39% helix, 16% strand | Q9UBT2 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.68 | 0.81 | 49 | empty |
| 2 | 469 | 0.66 | 0.78 | 62 | empty |
| 3 | 80 | 0.62 | 0.90 | 17 | empty |
| 4 | 266 | 0.53 | 0.76 | 35 | empty |
| 5 | 158 | 0.52 | 0.79 | 26 | empty |
Interfaces
1 interface between chains.
- C–D · 2520 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 6CWZ · Crystal structure of apo SUMO E1 · the same entry in another collection · chain C against C, TM-score 1.00
- 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 0.99
- 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 0.99
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 6CWZ · PDBe 6CWZ · UniProt Q9UBE0 · UniProt Q9UBT2
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