Research workbench
Structure of the MSL2 cxc domain bound with a non-specific (GC)6 DNA
Analyse Structure of the MSL2 cxc domain bound with a non-specific (GC)6 DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RKG
- Type
- protein + DNA
- Length
- 107 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase msl-2; DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')
- EC
- 6.3.2.-
- UniProt
- P50534
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase msl-2 (EC 6.3.2.-) | protein | 37 | 11% helix, 0% strand | P50534 |
| B | E3 ubiquitin-protein ligase msl-2 (EC 6.3.2.-) | protein | 46 | 9% helix, 0% strand | P50534 |
| H, I | DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.47 | 0.76 | 26 | empty |
| 2 | 75 | 0.32 | 0.76 | 12 | empty |
| 3 | 70 | 0.31 | 0.75 | 13 | empty |
Interfaces
5 interfaces between chains.
- H–I · 587 Ų buried · 62 hydrogen bonds · nucleic-nucleic
- B–I · 376 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–I · 315 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–H · 177 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–H · 132 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 4RKG · Structure of the MSL2 CXC domain bound with a non-specific (GC)6 DNA · the same entry in another collection · chain B against B, TM-score 1.00
- P50534 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase msl-2 (P50534) · a predicted model of the same protein · chain A 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 P50534
- Elsewhere: RCSB PDB 4RKG · PDBe 4RKG · UniProt P50534
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.