MolNFT v1 · #54832 · protein
Crystal structure of the human tatd-domain protein 3 (TATDN3)
2Y1H · Putative deoxyribonuclease TATDN3: “Crystal structure of the human tatd-domain protein 3 (TATDN3)”. X-ray diffraction, 3 ligands (ZN, NI, PO4), 5 pockets (best druggability 0.61). MolNFT v1 #54832 on GenesisL1: 3D structure, binding…
- PDB
- 2Y1H
- Type
- protein
- Length
- 527 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative deoxyribonuclease TATDN3
- EC
- 3.1.21.-
- UniProt
- Q17R31
- Ligands
- ZN, NI, PO4
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative deoxyribonuclease TATDN3 (EC 3.1.21.-) | protein | 262 | 51% helix, 15% strand | Q17R31 |
| B | Putative deoxyribonuclease TATDN3 (EC 3.1.21.-) | protein | 265 | 49% helix, 17% strand | Q17R31 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.61 | 0.92 | 19 | empty |
| 2 | 142 | 0.39 | 0.73 | 29 | PO4 |
| 3 | 91 | 0.36 | 0.75 | 25 | PO4 |
| 4 | 55 | 0.34 | 0.77 | 13 | empty |
| 5 | 52 | 0.32 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1234 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2Y1H · Crystal structure of the human TatD-domain protein 3 (TATDN3) · the same entry in another collection · chain A against A, TM-score 1.00
- Q17R31 · AlphaFold monomer V2.0 prediction for putative deoxyribonuclease TATDN3 (Q17R31) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 Q17R31
- Elsewhere: RCSB PDB 2Y1H · PDBe 2Y1H · UniProt Q17R31
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