MolNFT v1 · #116075 · protein
Complex between human SUMO2-RANGAP1, UBC9 and ZNF451
5D2M · Sumo-conjugating enzyme UBC9: “Complex between human SUMO2-RANGAP1, UBC9 and ZNF451”. X-ray diffraction, 9 pockets (best druggability 0.80). MolNFT v1 #116075 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5D2M
- Type
- protein
- Length
- 806 residues
- Chains
- 7
- 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, Q9Y4E5
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 157 | 34% helix, 20% strand | P63279 |
| B | Small ubiquitin-related modifier 2 | protein | 76 | 14% helix, 34% strand | P61956 |
| C | Ran GTPase-activating protein 1 | protein | 158 | 65% helix, 0% strand | P46060 |
| E | Small ubiquitin-related modifier 2 | protein | 80 | 18% helix, 36% strand | P61956 |
| F | Ran GTPase-activating protein 1 | protein | 157 | 65% helix, 0% strand | P46060 |
| G | Zinc finger protein 451 | protein | 21 | 0% helix, 62% strand | Q9Y4E5 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, E, G, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.80 | 0.81 | 91 | EDO |
| 2 | 213 | 0.55 | 0.79 | 30 | empty |
| 3 | 143 | 0.47 | 0.78 | 26 | empty |
| 4 | 148 | 0.43 | 0.75 | 23 | empty |
| 5 | 132 | 0.43 | 0.76 | 21 | empty |
Interfaces
13 interfaces between chains.
- A–B · 737 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 677 Ų buried · 13 hydrogen bonds · protein-protein
- E–G · 666 Ų buried · 9 hydrogen bonds · protein-protein
- B–G · 647 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 635 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- P46060 · AlphaFold monomer V2.0 prediction for ran GTPase-activating protein 1 (P46060) · a predicted model of the same protein · chain F 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 E against A, TM-score 0.95
- Q9Y4E5 · AlphaFold monomer V2.0 prediction for E3 sumo-protein ligase ZNF451 (Q9Y4E5) · a predicted model of the same protein · chain G against A, TM-score 0.19
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 Q9Y4E5
- Elsewhere: RCSB PDB 5D2M · PDBe 5D2M · UniProt P63279 · UniProt P61956 · UniProt P46060 · UniProt Q9Y4E5
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