Research workbench
Structure of the apo hoip pub domain
Analyse Structure of the apo hoip pub domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OYJ
- Type
- protein
- Length
- 2,333 residues
- Chains
- 13
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF31
- EC
- 6.3.2.-
- UniProt
- Q96EP0
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 182 | 60% helix, 5% strand | Q96EP0 |
| C, F | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 180 | 61% helix, 5% strand | Q96EP0 |
| D | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 182 | 60% helix, 5% strand | Q96EP0 |
| E, G | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 183 | 60% helix, 5% strand | Q96EP0 |
| H, I, K | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 178 | 61% helix, 5% strand | Q96EP0 |
| J, M | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 179 | 60% helix, 5% strand | Q96EP0 |
| L | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 169 | 58% helix, 5% strand | Q96EP0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 30 copies · chains A, M, E, B, C, D, F, G, H, I, K, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.74 | 0.77 | 80 | empty |
| 2 | 764 | 0.73 | 0.79 | 71 | SO4 |
| 3 | 1090 | 0.73 | 0.77 | 79 | empty |
| 4 | 816 | 0.71 | 0.77 | 96 | SO4 |
| 5 | 429 | 0.68 | 0.80 | 61 | SO4 |
Interfaces
23 interfaces between chains.
- A–E · 870 Ų buried · 13 hydrogen bonds · protein-protein
- K–L · 823 Ų buried · 15 hydrogen bonds · protein-protein
- B–J · 797 Ų buried · 13 hydrogen bonds · protein-protein
- C–K · 786 Ų buried · 17 hydrogen bonds · protein-protein
- D–I · 784 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 4OYJ · Structure of the apo HOIP PUB domain · the same entry in another collection · chain M against M, TM-score 1.00
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
- Elsewhere: RCSB PDB 4OYJ · PDBe 4OYJ · UniProt Q96EP0
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