Research workbench
Complex between human RANGAP1-SUMO2, UBC9 and the IR1 domain from RANBP2 containing IR2 motif II
Analyse Complex between human RANGAP1-SUMO2, UBC9 and the IR1 domain from RANBP2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UIO
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sumo-conjugating enzyme UBC9; Small ubiquitin-related modifier 2; Ran GTPase-activating…
- EC
- 6.3.2.-
- UniProt
- P63279, P61956, P46060, P49792
- Pockets
- 7 · best druggability 0.55
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 156 | 34% helix, 21% strand | P63279 |
| B | Small ubiquitin-related modifier 2 | protein | 79 | 14% helix, 35% strand | P61956 |
| C | Ran GTPase-activating protein 1 | protein | 156 | 67% helix, 0% strand | P46060 |
| D | E3 sumo-protein ligase RANBP2 | protein | 65 | 34% helix, 9% 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 | 243 | 0.55 | 0.77 | 42 | empty |
| 2 | 134 | 0.52 | 0.81 | 26 | empty |
| 3 | 105 | 0.41 | 0.77 | 16 | empty |
| 4 | 79 | 0.37 | 0.76 | 18 | empty |
| 5 | 68 | 0.35 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1395 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 609 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 604 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 604 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 53 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 modified, 1 isopeptide (oxidation, isopeptide).
Compared structures
- 3UIO · Complex between human RanGAP1-SUMO2, 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 0.98
- 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 0.97
- P61956 · AlphaFold monomer V2.0 prediction for small ubiquitin-related modifier 2 (P61956) · 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 P61956
- Every structure of UniProt P46060
- Every structure of UniProt P49792
- Elsewhere: RCSB PDB 3UIO · PDBe 3UIO · UniProt P63279 · UniProt P61956 · UniProt P46060 · UniProt P49792
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