Research workbench
Crystal structure of the B2 box from MURF1 in dimeric state
Analyse Crystal structure of the B2 box from MURF1 in dimeric state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DDT
- Type
- protein
- Length
- 139 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase TRIM63
- EC
- 6.3.2.-
- UniProt
- Q969Q1
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase TRIM63 (EC 6.3.2.-) | protein | 48 | 13% helix, 23% strand | Q969Q1 |
| B | E3 ubiquitin-protein ligase TRIM63 (EC 6.3.2.-) | protein | 47 | 11% helix, 23% strand | Q969Q1 |
| C | E3 ubiquitin-protein ligase TRIM63 (EC 6.3.2.-) | protein | 44 | 11% helix, 25% strand | Q969Q1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 350 | 0.58 | 0.76 | 31 | empty |
| 2 | 54 | 0.32 | 0.77 | 15 | empty |
| 3 | 52 | 0.26 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 540 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 74 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 44 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3DDT · Crystal structure of the B2 box from MuRF1 in dimeric state · the same entry in another collection · chain A against A, TM-score 1.00
- Q969Q1 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM63 (Q969Q1) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 Q969Q1
- Elsewhere: RCSB PDB 3DDT · PDBe 3DDT · UniProt Q969Q1
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