Research workbench
Crystal structure of the human RPAP3(TPR2)-PIH1D1(CS) complex
Analyse Crystal structure of the human RPAP3(TPR2)-PIH1D1(CS) complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GXZ
- Type
- protein
- Length
- 479 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.965
- Source
- Homo sapiens
- Molecule
- RNA polymerase II-associated protein 3; PIH1 domain-containing protein 1
- UniProt
- Q9H6T3, Q9NWS0
- Ligands
- CA
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · resolution 2.965 · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA polymerase II-associated protein 3 | protein | 149 | 65% helix, 5% strand | Q9H6T3 |
| C | RNA polymerase II-associated protein 3 | protein | 156 | 65% helix, 6% strand | Q9H6T3 |
| D | PIH1 domain-containing protein 1 | protein | 88 | 0% helix, 48% strand | Q9NWS0 |
| E | PIH1 domain-containing protein 1 | protein | 86 | 0% helix, 49% strand | Q9NWS0 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.33 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1777 Ų buried · 21 hydrogen bonds · protein-protein
- A–E · 1633 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 320 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6GXZ · Crystal structure of the human RPAP3(TPR2)-PIH1D1(CS) complex · the same entry in another collection · chain E against E, TM-score 1.00
- Q9NWS0 · AlphaFold monomer V2.0 prediction for PIH1 domain-containing protein 1 (Q9NWS0) · a predicted model of the same protein · chain E against A, TM-score 0.97
- Q9H6T3 · AlphaFold monomer V2.0 prediction for RNA polymerase II-associated protein 3 (Q9H6T3) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 Q9H6T3
- Every structure of UniProt Q9NWS0
- Elsewhere: RCSB PDB 6GXZ · PDBe 6GXZ · UniProt Q9H6T3 · UniProt Q9NWS0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.