MolNFT v1 · #123538 · protein
E2-sumo-SIZ1 E3-sumo-PCNA complex
5JNE · E3 sumo-protein ligase SIZ1,UBIQUITIN-like protein SMT3: “E2-sumo-SIZ1 E3-sumo-PCNA complex”. X-ray diffraction, 2 ligands (6LN, ZN), 19 pockets (best druggability 0.75). MolNFT v1 #123538 on GenesisL1: 3D structure, binding sites…
- PDB
- 5JNE
- Type
- protein
- Length
- 1,678 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 sumo-protein ligase SIZ1,UBIQUITIN-like protein SMT3; Sumo-conjugating enzyme UBC9…
- EC
- 6.3.2.-
- UniProt
- Q04195, Q12306, P50623, P15873
- Ligands
- 6LN, ZN
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 8 distinct chains · 22% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 sumo-protein ligase SIZ1,UBIQUITIN-like protein SMT3 (EC 6.3.2.-) | protein | 351 | 21% helix, 34% strand | Q04195, Q12306 |
| B | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 157 | 34% helix, 18% strand | P50623 |
| C | Ubiquitin-like protein SMT3 | protein | 79 | 16% helix, 37% strand | Q12306 |
| D | Proliferating cell nuclear antigen | protein | 254 | 18% helix, 43% strand | P15873 |
| E | E3 sumo-protein ligase SIZ1,UBIQUITIN-like protein SMT3 (EC 6.3.2.-) | protein | 348 | 21% helix, 37% strand | Q04195, Q12306 |
| F | Sumo-conjugating enzyme UBC9 (EC 6.3.2.-) | protein | 156 | 34% helix, 19% strand | P50623 |
| G | Ubiquitin-like protein SMT3 | protein | 77 | 17% helix, 38% strand | Q12306 |
| H | Proliferating cell nuclear antigen | protein | 256 | 17% helix, 45% strand | P15873 |
Ligands and binding sites
- 6LN · ethane-1,2-dithiol · ligand · 2 copies · chains B, C, D, F, G, H
- ZN · Zinc ion · metal · 2 copies · chains A, E
- GOL · Glycerol · additive · 10 copies · chains A, D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.75 | 0.81 | 74 | empty |
| 2 | 1147 | 0.74 | 0.77 | 80 | GOL |
| 3 | 574 | 0.73 | 0.81 | 65 | empty |
| 4 | 937 | 0.71 | 0.76 | 77 | GOL |
| 5 | 57 | 0.70 | 0.97 | 18 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1422 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1415 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 885 Ų buried · 11 hydrogen bonds · protein-protein
- E–G · 817 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 577 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 isopeptide (covalent ligand, isopeptide).
Compared structures
- 5JNE · E2-SUMO-Siz1 E3-SUMO-PCNA complex · the same entry in another collection · chain H against H, TM-score 1.00
- P50623 · AlphaFold monomer V2.0 prediction for sumo-conjugating enzyme UBC9 (P50623) · a predicted model of the same protein · chain F against A, TM-score 0.96
- Q12306 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein SMT3 (Q12306) · a predicted model of the same protein · chain G 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 Q04195
- Every structure of UniProt Q12306
- Every structure of UniProt P50623
- Every structure of UniProt P15873
- Elsewhere: RCSB PDB 5JNE · PDBe 5JNE · UniProt Q04195 · UniProt Q12306 · UniProt P50623 · UniProt P15873
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