Research workbench
Crystal structure of hoip RING1 domain bound to IPAH1.4 lrr domain
Analyse Crystal structure of hoip RING1 domain bound to IPAH1.4 lrr domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7V8G
- Type
- protein
- Length
- 653 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ring-type E3 ubiquitin transferase; E3 ubiquitin-protein ligase RNF31
- EC
- 2.3.2.27, 2.3.2.31
- UniProt
- Q9AFJ5, Q96EP0
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 32% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ring-type E3 ubiquitin transferase (EC 2.3.2.27) | protein | 235 | 17% helix, 13% strand | Q9AFJ5 |
| D | E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31) | protein | 90 | 48% helix, 4% strand | Q96EP0 |
| C | E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31) | protein | 93 | 54% helix, 11% strand | Q96EP0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 265 | 0.73 | 0.86 | 38 | empty |
| 2 | 222 | 0.55 | 0.78 | 37 | empty |
| 3 | 219 | 0.55 | 0.78 | 36 | empty |
| 4 | 173 | 0.46 | 0.75 | 26 | empty |
| 5 | 140 | 0.45 | 0.76 | 27 | empty |
Interfaces
2 interfaces between chains.
- A–C · 651 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 536 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7V8G · Crystal structure of HOIP RING1 domain bound to IpaH1.4 LRR domain · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.97
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 Q9AFJ5
- Every structure of UniProt Q96EP0
- Elsewhere: RCSB PDB 7V8G · PDBe 7V8G · UniProt Q9AFJ5 · UniProt Q96EP0
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