Research workbench
Complex between human RANGAP1-SUMO2, UBC9 and the IR1 domain from RANBP2
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
- 3UIN
- 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 0.64
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 | 157 | 34% helix, 20% strand | P63279 |
| B | Small ubiquitin-related modifier 2 | protein | 78 | 19% helix, 33% strand | P61956 |
| C | Ran GTPase-activating protein 1 | protein | 156 | 66% helix, 0% strand | P46060 |
| D | E3 sumo-protein ligase RANBP2 | protein | 65 | 32% helix, 8% 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 | 399 | 0.64 | 0.78 | 50 | empty |
| 2 | 123 | 0.51 | 0.81 | 27 | empty |
| 3 | 92 | 0.45 | 0.80 | 17 | empty |
| 4 | 73 | 0.36 | 0.77 | 18 | empty |
| 5 | 74 | 0.33 | 0.75 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1408 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 625 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 604 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 55 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 3UIN · Complex between human RanGAP1-SUMO2, UBC9 and the IR1 domain from RanBP2 · 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 0.95
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 P61956
- Every structure of UniProt P46060
- Every structure of UniProt P49792
- Elsewhere: RCSB PDB 3UIN · PDBe 3UIN · UniProt P63279 · UniProt P61956 · UniProt P46060 · UniProt P49792
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