MolNFT v1 · #81172 · protein
Complex between human RANGAP1-SUMO1, UBC9 and the IR1 domain from RANBP2 containing IR2 motif II
3UIP · Sumo-conjugating enzyme UBC9: “Complex between human RANGAP1-SUMO1, UBC9 and the IR1 domain from RANBP2 containing IR2 motif II”. X-ray diffraction, 7 pockets (best druggability 0.64). MolNFT v1 #81172 on GenesisL1: 3D structure…
- PDB
- 3UIP
- Type
- protein
- Length
- 452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sumo-conjugating enzyme UBC9; Small ubiquitin-related modifier 1; Ran GTPase-activating…
- EC
- 6.3.2.-
- UniProt
- P63279, P63165, P46060, P49792
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 157 | 34% helix, 20% strand | P63279 |
| B | Small ubiquitin-related modifier 1 | protein | 78 | 23% helix, 37% strand | P63165 |
| C | Ran GTPase-activating protein 1 | protein | 156 | 65% helix, 0% strand | P46060 |
| D | E3 sumo-protein ligase RANBP2 | protein | 61 | 33% helix, 10% strand | P49792 |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 418 | 0.64 | 0.77 | 46 | empty |
| 2 | 198 | 0.50 | 0.77 | 29 | empty |
| 3 | 117 | 0.41 | 0.76 | 23 | empty |
| 4 | 77 | 0.38 | 0.78 | 16 | empty |
| 5 | 59 | 0.31 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1464 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 707 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 660 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 644 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 54 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified, 1 isopeptide (artifact, isopeptide, oxidation).
Compared structures
- 3UIP · Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2… · the same entry in another collection · chain A against A, TM-score 1.00
- P46060 · AlphaFold monomer V2.0 prediction for ran GTPase-activating protein 1 (P46060) · a predicted model of the same protein · chain C against A, TM-score 0.99
- 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
- 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 0.94
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 P63165
- Every structure of UniProt P46060
- Every structure of UniProt P49792
- Elsewhere: RCSB PDB 3UIP · PDBe 3UIP · UniProt P63279 · UniProt P63165 · UniProt P46060 · UniProt P49792
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