Research workbench
Crystal structure of the DUF55 domain of human thymocyte nuclear protein 1
Analyse Crystal structure of the DUF55 domain of human thymocyte nuclear protein 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EOP
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thymocyte nuclear protein 1
- UniProt
- Q9P016
- Ligands
- SO4
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thymocyte nuclear protein 1 | protein | 169 | 29% helix, 31% strand | Q9P016 |
| B | Thymocyte nuclear protein 1 | protein | 161 | 32% helix, 27% strand | Q9P016 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.76 | 0.79 | 78 | SO4 |
Interfaces
1 interface between chains.
- A–B · 382 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3EOP · Crystal Structure of the DUF55 domain of human thymocyte nuclear protein 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9P016 · AlphaFold monomer V2.0 prediction for thymocyte nuclear protein 1 (Q9P016) · a predicted model of the same protein · chain A 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 Q9P016
- Elsewhere: RCSB PDB 3EOP · PDBe 3EOP · UniProt Q9P016
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