Research workbench
Crystal structure of human sumo E2-conjugating enzyme (UBC9) in complex with E1-activating enzyme (UBA2) ubiquitin fold domain (ufd)
Analyse Crystal structure of human sumo E2-conjugating enzyme (UBC9) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4W5V
- Type
- protein
- Length
- 264 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sumo-conjugating enzyme UBC9; Sumo-activating enzyme subunit 2
- EC
- 6.3.2.-
- UniProt
- P63279, Q9UBT2
- Ligands
- K
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 158 | 35% helix, 21% strand | P63279 |
| B | Sumo-activating enzyme subunit 2 (EC 6.3.2.-) | protein | 106 | 15% helix, 33% strand | Q9UBT2 |
Ligands and binding sites
- K · Potassium ion · metal · chains B
- FMT · Formic acid · additive · chains A
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.60 | 0.92 | 14 | empty |
| 2 | 55 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 767 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4W5V · Crystal structure of Human SUMO E2-conjugating enzyme (Ubc9) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P63279 · AlphaFold monomer V2.0 prediction for sumo-conjugating enzyme UBC9 (P63279) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9UBT2 · AlphaFold monomer V2.0 prediction for sumo-activating enzyme subunit 2 (Q9UBT2) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P63279
- Every structure of UniProt Q9UBT2
- Elsewhere: RCSB PDB 4W5V · PDBe 4W5V · UniProt P63279 · UniProt Q9UBT2
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