MolNFT v1 · #184836 · protein
Structure of the E3 ligase SMC5/NSE2 in complex with UBC9-sumo thioester mimetic
7P47 · Structural maintenance of chromosomes protein 5: “Structure of the E3 ligase SMC5/NSE2 in complex with UBC9-sumo thioester mimetic”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.78). MolNFT v1 #184836 on…
- PDB
- 7P47
- Type
- protein
- Length
- 562 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Structural maintenance of chromosomes protein 5; Sumo-conjugating enzyme UBC9; E3…
- EC
- 2.3.2.-
- UniProt
- Q08204, P50623, P38632, Q12306
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Structural maintenance of chromosomes protein 5 | protein | 69 | 88% helix, 0% strand | Q08204 |
| C | Sumo-conjugating enzyme UBC9 (EC 2.3.2.-) | protein | 155 | 32% helix, 20% strand | P50623 |
| A | E3 sumo-protein ligase MMS21 (EC 2.3.2.-) | protein | 187 | 47% helix, 12% strand | P38632 |
| E | Ubiquitin-like protein SMT3 | protein | 73 | 19% helix, 33% strand | Q12306 |
| D | Ubiquitin-like protein SMT3 | protein | 78 | 14% helix, 35% strand | Q12306 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 786 | 0.78 | 0.82 | 73 | empty |
| 2 | 118 | 0.54 | 0.82 | 20 | empty |
| 3 | 130 | 0.49 | 0.79 | 21 | empty |
| 4 | 182 | 0.49 | 0.76 | 36 | empty |
| 5 | 126 | 0.44 | 0.77 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–A · 1195 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 952 Ų buried · 16 hydrogen bonds · protein-protein
- C–A · 643 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 590 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 524 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 7P47 · Structure of the E3 ligase Smc5/Nse2 in complex with Ubc9-SUMO thioester mimetic · the same entry in another collection · chain D against D, TM-score 1.00
- P50623 · AlphaFold monomer V2.0 prediction for sumo-conjugating enzyme UBC9 (P50623) · a predicted model of the same protein · chain C 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 E against A, TM-score 0.93
- Q08204 · AlphaFold monomer V2.0 prediction for structural maintenance of chromosomes protein 5… · a predicted model of the same protein · chain B against A, TM-score 0.78
- P38632 · AlphaFold monomer V2.0 prediction for E3 sumo-protein ligase MMS21 (P38632) · a predicted model of the same protein · chain A against A, TM-score 0.76
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 Q08204
- Every structure of UniProt P50623
- Every structure of UniProt P38632
- Every structure of UniProt Q12306
- Elsewhere: RCSB PDB 7P47 · PDBe 7P47 · UniProt Q08204 · UniProt P50623 · UniProt P38632 · UniProt Q12306
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