Research workbench
Structure of DSE3-CSM1 complex
Analyse Structure of DSE3-CSM1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DEI
- Type
- protein
- Length
- 253 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monopolin complex subunit CSM1; Protein DSE3
- UniProt
- P25651, Q08729
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monopolin complex subunit CSM1 | protein | 107 | 42% helix, 38% strand | P25651 |
| B | Monopolin complex subunit CSM1 | protein | 105 | 38% helix, 32% strand | P25651 |
| C | Protein DSE3 | protein | 24 | 13% helix, 8% strand | Q08729 |
| D | Protein DSE3 | protein | 17 | 47% helix, 0% strand | Q08729 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.45 | 0.79 | 22 | empty |
| 2 | 101 | 0.43 | 0.78 | 17 | empty |
| 3 | 64 | 0.42 | 0.81 | 16 | empty |
| 4 | 50 | 0.33 | 0.78 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1194 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 754 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 711 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 121 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6DEI · Structure of Dse3-Csm1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- P25651 · AlphaFold monomer V2.0 prediction for monopolin complex subunit CSM1 (P25651) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q08729 · AlphaFold monomer V2.0 prediction for protein DSE3 (Q08729) · a predicted model of the same protein · chain D against A, TM-score 0.32
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 P25651
- Every structure of UniProt Q08729
- Elsewhere: RCSB PDB 6DEI · PDBe 6DEI · UniProt P25651 · UniProt Q08729
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.