MolNFT v1 · #105946 · protein + DNA
Structure of the MSL2 cxc domain bound with a specific mre sequence
4RKH · E3 ubiquitin-protein ligase msl-2: “Structure of the MSL2 cxc domain bound with a specific mre sequence”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.71). MolNFT v1 #105946 on GenesisL1: 3D structure, binding…
- PDB
- 4RKH
- Type
- protein + DNA
- Length
- 225 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase msl-2; DNA (5'-D(*AP*TP*GP*AP*GP*CP*GP*AP*GP*AP*TP*GP*GP*AP*T)…
- EC
- 6.3.2.-
- UniProt
- P50534
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 10% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | E3 ubiquitin-protein ligase msl-2 (EC 6.3.2.-) | protein | 47 | 15% helix, 0% strand | P50534 |
| D | E3 ubiquitin-protein ligase msl-2 (EC 6.3.2.-) | protein | 51 | 8% helix, 0% strand | P50534 |
| E | E3 ubiquitin-protein ligase msl-2 (EC 6.3.2.-) | protein | 51 | 8% helix, 0% strand | P50534 |
| F | E3 ubiquitin-protein ligase msl-2 (EC 6.3.2.-) | protein | 46 | 9% helix, 0% strand | P50534 |
| A | DNA (5'-D(*AP*TP*GP*AP*GP*CP*GP*AP*GP*AP*TP*GP*GP*AP*T)- 3') | dna | 15 | — | — |
| B | DNA (5'-D(*AP*TP*CP*CP*AP*TP*CP*TP*CP*GP*CP*TP*CP*AP*T)- 3') | dna | 15 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 183 | 0.71 | 0.89 | 31 | empty |
| 2 | 407 | 0.66 | 0.80 | 47 | empty |
| 3 | 211 | 0.53 | 0.78 | 24 | empty |
| 4 | 82 | 0.31 | 0.74 | 12 | empty |
Interfaces
11 interfaces between chains.
- A–B · 670 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- F–B · 398 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–B · 395 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–A · 367 Ų buried · 8 hydrogen bonds · protein-nucleic
- E–A · 351 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 4RKH · Structure of the MSL2 CXC domain bound with a specific MRE sequence · 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 F against A, TM-score 0.48
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 4RKH · PDBe 4RKH · UniProt P50534
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