MolNFT v1 · #93472 · protein
Crystal structure of a ternary complex of human symplekin ntd, human SSU72 and a RNA poymerase II ctd peptide phosphorylated at ser-7
4H3H: “Crystal structure of a ternary complex of human symplekin ntd, human SSU72 and a RNA poymerase II ctd peptide…”. X-ray diffraction, 1 ligand (PO4), 7 pockets (best druggability 0.75). MolNFT v1 #93472 on GenesisL1: 3D structure…
- PDB
- 4H3H
- Type
- protein
- Length
- 1,017 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; Pol II ctd…
- EC
- 3.1.3.16
- UniProt
- Q92797, Q9NP77
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 65% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Symplekin | protein | 317 | 76% helix, 0% strand | Q92797 |
| B | RNA polymerase II subunit a C-terminal domain phosphatase SSU72 (EC 3.1.3.16) | protein | 189 | 49% helix, 18% strand | Q9NP77 |
| D | Symplekin | protein | 311 | 77% helix, 0% strand | Q92797 |
| E | RNA polymerase II subunit a C-terminal domain phosphatase SSU72 (EC 3.1.3.16) | protein | 192 | 47% helix, 18% strand | Q9NP77 |
| F | Pol II ctd peptide | protein | 8 | 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.75 | 0.84 | 61 | empty |
| 2 | 418 | 0.72 | 0.83 | 51 | empty |
| 3 | 392 | 0.66 | 0.79 | 36 | empty |
| 4 | 495 | 0.60 | 0.75 | 47 | empty |
| 5 | 328 | 0.58 | 0.77 | 35 | empty |
Interfaces
4 interfaces between chains.
- D–E · 1217 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1185 Ų buried · 15 hydrogen bonds · protein-protein
- E–F · 565 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 314 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 4H3H · Crystal structure of a ternary complex of human symplekin NTD, human Ssu72 and a RNA… · the same entry in another collection · chain D against D, 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 4H3H · PDBe 4H3H · UniProt Q92797 · UniProt Q9NP77
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