Research workbench
Crystal structure of the pabc-TNRC6C complex
Analyse Crystal structure of the pabc-TNRC6C complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X04
- Type
- protein
- Length
- 186 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyadenylate-binding protein 1; Trinucleotide repeat-containing gene 6C protein
- UniProt
- P11940, Q9HCJ0
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polyadenylate-binding protein 1 | protein | 77 | 73% helix, 0% strand | P11940 |
| B | Polyadenylate-binding protein 1 | protein | 79 | 76% helix, 0% strand | P11940 |
| C, D | Trinucleotide repeat-containing gene 6C protein | protein | 15 | 0% helix, 0% strand | Q9HCJ0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B
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 | 86 | 0.46 | 0.81 | 21 | empty |
| 2 | 78 | 0.36 | 0.76 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–C · 589 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 588 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 312 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 217 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 88 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2X04 · Crystal structure of the PABC-TNRC6C complex · the same entry in another collection · chain A against A, TM-score 1.00
- P11940 · AlphaFold monomer V2.0 prediction for polyadenylate-binding protein 1 (P11940) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q9HCJ0 · AlphaFold monomer V2.0 prediction for trinucleotide repeat-containing gene 6C protein… · a predicted model of the same protein · chain C against A, TM-score 0.32
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 P11940
- Every structure of UniProt Q9HCJ0
- Elsewhere: RCSB PDB 2X04 · PDBe 2X04 · UniProt P11940 · UniProt Q9HCJ0
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