Research workbench
Crystal structure of a complex between UBC9, sumo-1, RANGAP1 and NUP358/RANBP2
Analyse Crystal structure of a complex between UBC9, sumo-1, RANGAP1 and NUP358/RANBP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z5S
- Type
- protein
- Length
- 455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 I; Ubiquitin-like protein SMT3C; Ran GTPase-activating…
- EC
- 6.3.2.19
- UniProt
- P63279, P63165, P46060, P49792
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 I (EC 6.3.2.19) | protein | 156 | 33% helix, 20% strand | P63279 |
| B | Ubiquitin-like protein SMT3C | protein | 78 | 18% helix, 27% strand | P63165 |
| C | Ran GTPase-activating protein 1 | protein | 156 | 60% helix, 0% strand | P46060 |
| D | Ran-binding protein 2 | protein | 65 | 25% 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 | 368 | 0.64 | 0.79 | 60 | empty |
| 2 | 182 | 0.57 | 0.81 | 28 | empty |
| 3 | 109 | 0.40 | 0.76 | 22 | empty |
| 4 | 84 | 0.34 | 0.74 | 12 | empty |
| 5 | 64 | 0.31 | 0.75 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–D · 1258 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 744 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 654 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 583 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 54 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 1Z5S · Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/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 0.96
- 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 0.92
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 1Z5S · PDBe 1Z5S · UniProt P63279 · UniProt P63165 · UniProt P46060 · UniProt P49792
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