MolNFT v1 · #12725 · protein
Structural basis for E2-mediated sumo conjugation revealed by a complex between ubiquitin conjugating enzyme UBC9 and RANGAP1
1KPS · Ubiquitin-like protein sumo-1 conjugating enzyme: “Structural basis for E2-mediated sumo conjugation revealed by a complex between ubiquitin conjugating enzyme…”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability…
- PDB
- 1KPS
- Type
- protein
- Length
- 626 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-like protein sumo-1 conjugating enzyme; Ran-GTPase activating protein 1
- EC
- 6.3.2.19
- UniProt
- P63279, P46061
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-like protein sumo-1 conjugating enzyme (EC 6.3.2.19) | protein | 159 | 33% helix, 21% strand | P63279 |
| B | Ran-GTPase activating protein 1 | protein | 156 | 63% helix, 0% strand | P46061 |
| C | Ubiquitin-like protein sumo-1 conjugating enzyme (EC 6.3.2.19) | protein | 156 | 34% helix, 21% strand | P63279 |
| D | Ran-GTPase activating protein 1 | protein | 155 | 63% helix, 0% strand | P46061 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.47 | 0.75 | 34 | empty |
| 2 | 177 | 0.45 | 0.75 | 36 | empty |
| 3 | 99 | 0.36 | 0.75 | 20 | empty |
| 4 | 63 | 0.30 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 633 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 628 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 574 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 279 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 245 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1KPS · Structural Basis for E2-mediated SUMO conjugation revealed by a complex between ubiquitin… · 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
- P46061 · AlphaFold monomer V2.0 prediction for ran GTPase-activating protein 1 (P46061) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P46061
- Elsewhere: RCSB PDB 1KPS · PDBe 1KPS · UniProt P63279 · UniProt P46061
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