MolNFT v1 · #70684 · protein
Crystal structure of the U-box domain of human ubiquitin-protein ligase (E3), northeast structural genomics consortium target HR4604D.
3LRQ · E3 ubiquitin-protein ligase TRIM37: “Crystal structure of the U-box domain of human ubiquitin-protein ligase (E3), northeast structural genomics…”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.53). MolNFT v1…
- PDB
- 3LRQ
- Type
- protein
- Length
- 328 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase TRIM37
- EC
- 6.3.2.-
- UniProt
- O94972
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase TRIM37 (EC 6.3.2.-) | protein | 82 | 44% helix, 15% strand | O94972 |
| B | E3 ubiquitin-protein ligase TRIM37 (EC 6.3.2.-) | protein | 80 | 43% helix, 15% strand | O94972 |
| C | E3 ubiquitin-protein ligase TRIM37 (EC 6.3.2.-) | protein | 82 | 41% helix, 15% strand | O94972 |
| D | E3 ubiquitin-protein ligase TRIM37 (EC 6.3.2.-) | protein | 84 | 43% helix, 14% strand | O94972 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.53 | 0.75 | 41 | empty |
| 2 | 134 | 0.42 | 0.75 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1107 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1046 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 240 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3LRQ · Crystal structure of the U-box domain of human ubiquitin-protein ligase (E3), NORTHEAST… · the same entry in another collection · chain D against D, TM-score 1.00
- O94972 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM37 (O94972) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 O94972
- Elsewhere: RCSB PDB 3LRQ · PDBe 3LRQ · UniProt O94972
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