Research workbench
SSU72/SYMPK in complex with SER2/SER5 phosphorylated peptide
Analyse SSU72/SYMPK in complex with SER2/SER5 phosphorylated peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NPW
- Type
- protein
- Length
- 1,041 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Symplekin; SSU72 ortholog, LD40846P; SER2/SER5 phosphorylated peptide
- EC
- 3.1.3.-, 3.1.3.16, 3.1.3.41
- UniProt
- Q8MSU4, Q9VWE4
- Ligands
- PO4
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Symplekin | protein | 332 | 75% helix, 0% strand | Q8MSU4 |
| B, D | SSU72 ortholog, LD40846P (EC 3.1.3.-, 3.1.3.16, 3.1.3.41) | protein | 192 | 43% helix, 19% strand | Q9VWE4 |
| C | Symplekin | protein | 320 | 71% helix, 0% strand | Q8MSU4 |
| E | SER2/SER5 phosphorylated peptide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.75 | 0.82 | 46 | empty |
| 2 | 345 | 0.74 | 0.86 | 50 | empty |
| 3 | 335 | 0.73 | 0.85 | 51 | empty |
| 4 | 450 | 0.66 | 0.79 | 37 | empty |
| 5 | 348 | 0.62 | 0.78 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1299 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1261 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 856 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 408 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
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 Q8MSU4
- Every structure of UniProt Q9VWE4
- Elsewhere: RCSB PDB 6NPW · PDBe 6NPW · UniProt Q8MSU4 · UniProt Q9VWE4
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