Research workbench
Crystal structure of the human symplekin-SSU72-ctd phosphopeptide complex
Analyse Crystal structure of the human symplekin-SSU72-ctd phosphopeptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O2Q
- Type
- protein
- Length
- 1,015 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Symplekin; RNA polymerase II subunit a C-terminal domain phosphatase SSU72; RNA…
- EC
- 3.1.3.16
- UniProt
- Q92797, Q9NP77
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 65% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Symplekin | protein | 317 | 75% helix, 0% strand | Q92797 |
| B | RNA polymerase II subunit a C-terminal domain phosphatase SSU72 (EC 3.1.3.16) | protein | 189 | 48% helix, 20% strand | Q9NP77 |
| D | Symplekin | protein | 311 | 76% helix, 0% strand | Q92797 |
| E | RNA polymerase II subunit a C-terminal domain phosphatase SSU72 (EC 3.1.3.16) | protein | 192 | 47% helix, 19% strand | Q9NP77 |
| F | RNA polymerase II ctd serine-5 phosphopeptide | protein | 6 | 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
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.71 | 0.83 | 51 | empty |
| 2 | 465 | 0.67 | 0.79 | 45 | empty |
| 3 | 285 | 0.66 | 0.82 | 38 | empty |
| 4 | 142 | 0.65 | 0.87 | 26 | empty |
| 5 | 420 | 0.59 | 0.75 | 42 | empty |
Interfaces
4 interfaces between chains.
- D–E · 1244 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1210 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 510 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 315 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 3O2Q · Crystal structure of the human symplekin-Ssu72-CTD phosphopeptide complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q9NP77 · AlphaFold monomer V2.0 prediction for RNA polymerase II subunit a C-terminal domain… · a predicted model of the same protein · chain E against A, TM-score 0.99
- Q92797 · AlphaFold monomer V2.0 prediction for symplekin (Q92797) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q92797
- Every structure of UniProt Q9NP77
- Elsewhere: RCSB PDB 3O2Q · PDBe 3O2Q · UniProt Q92797 · UniProt Q9NP77
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