MolNFT v1 · #125795 · protein
Structure of the hoip pub domain bound to SPATA2 pim peptide
5LJN · E3 ubiquitin-protein ligase RNF31: “Structure of the hoip pub domain bound to SPATA2 pim peptide”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.61). MolNFT v1 #125795 on GenesisL1: 3D structure, binding sites…
- PDB
- 5LJN
- Type
- protein
- Length
- 349 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF31; Spermatogenesis-associated protein 2
- EC
- 6.3.2.-
- UniProt
- Q96EP0, Q9UM82
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 173 | 59% helix, 5% strand | Q96EP0 |
| B | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 161 | 60% helix, 5% strand | Q96EP0 |
| C | Spermatogenesis-associated protein 2 | protein | 8 | 0% helix, 0% strand | Q9UM82 |
| D | Spermatogenesis-associated protein 2 | protein | 7 | 0% helix, 0% strand | Q9UM82 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.61 | 0.89 | 18 | GOL |
| 2 | 259 | 0.57 | 0.78 | 32 | empty |
| 3 | 163 | 0.44 | 0.76 | 29 | empty |
| 4 | 64 | 0.31 | 0.75 | 19 | empty |
| 5 | 55 | 0.25 | 0.73 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–C · 501 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 471 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 466 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 194 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 147 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5LJN · Structure of the HOIP PUB domain bound to SPATA2 PIM peptide · the same entry in another collection · chain D against D, TM-score 1.00
- Q96EP0 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF31 (Q96EP0) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9UM82 · AlphaFold monomer V2.0 prediction for spermatogenesis-associated protein 2 (Q9UM82) · a predicted model of the same protein · chain D against A, TM-score 0.49
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 Q96EP0
- Every structure of UniProt Q9UM82
- Elsewhere: RCSB PDB 5LJN · PDBe 5LJN · UniProt Q96EP0 · UniProt Q9UM82
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