Research workbench
Crystal structure of the drosophila melanogaster SSU72-pctd complex
Analyse Crystal structure of the drosophila melanogaster SSU72-pctd complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P9Y
- Type
- protein
- Length
- 808 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG14216; PSER5 ctd peptide
- UniProt
- Q9VWE4
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | CG14216 | protein | 198 | 45% helix, 18% strand | Q9VWE4 |
| C | CG14216 | protein | 193 | 47% helix, 18% strand | Q9VWE4 |
| D | CG14216 | protein | 191 | 47% helix, 23% strand | Q9VWE4 |
| E, F, G, H | PSER5 ctd peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- IMD · Imidazole · additive · 4 copies · chains A, D, B, C, G
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.80 | 0.86 | 87 | IMD |
| 2 | 499 | 0.78 | 0.86 | 79 | IMD |
| 3 | 171 | 0.47 | 0.76 | 35 | empty |
| 4 | 74 | 0.40 | 0.79 | 12 | empty |
| 5 | 62 | 0.38 | 0.79 | 15 | empty |
Interfaces
18 interfaces between chains.
- A–C · 605 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 588 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 529 Ų buried · 16 hydrogen bonds · protein-protein
- D–H · 527 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 526 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (nonstandard, phosphorylation).
Compared structures
- 3P9Y · Crystal structure of the Drosophila melanogaster Ssu72-pCTD complex · 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 Q9VWE4
- Elsewhere: RCSB PDB 3P9Y · PDBe 3P9Y · UniProt Q9VWE4
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