Research workbench
Structure of SCP1 D96N bound to rest-PS861/4 peptide
Analyse Structure of SCP1 D96N bound to rest-PS861/4 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DU2
- Type
- protein
- Length
- 372 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 1 isoform X2…
- UniProt
- A0A1S2ZIN9
- Ligands
- MG
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Carboxy-terminal domain RNA polymerase II polypeptide a small phosphatase 1 isoform X2 | protein | 180 | 32% helix, 27% strand | A0A1S2ZIN9 |
| C | Rest-PS861/4 | protein | 6 | 0% helix, 0% strand | — |
| D | Rest-PS861/4 | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, C, B, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 103 | 0.38 | 0.76 | 26 | empty |
| 2 | 55 | 0.31 | 0.76 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 552 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 441 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 419 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 6DU2 · Structure of Scp1 D96N bound to REST-pS861/4 peptide · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A1S2ZIN9
- Elsewhere: RCSB PDB 6DU2 · PDBe 6DU2 · UniProt A0A1S2ZIN9
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