MolNFT v1 · #34857 · protein
Crystal structure of TTHA1657 (at-rich DNA-binding protein) from thermus thermophilus HB8
2DT5: “Crystal structure of TTHA1657 (at-rich DNA-binding protein) from thermus thermophilus HB8”. X-ray diffraction, 3 ligands (NAD, SO4, CL), 4 pockets (best druggability 0.75). MolNFT v1 #34857 on GenesisL1: 3D structure, binding sites…
- PDB
- 2DT5
- Type
- protein
- Length
- 421 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- At-rich DNA-binding protein
- UniProt
- Q5SHS3
- Ligands
- NAD, SO4, CL
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | At-rich DNA-binding protein | protein | 210 | 45% helix, 18% strand | Q5SHS3 |
| B | At-rich DNA-binding protein | protein | 211 | 39% helix, 17% strand | Q5SHS3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.75 | 0.79 | 82 | CL |
| 2 | 264 | 0.66 | 0.82 | 35 | NAD |
| 3 | 250 | 0.61 | 0.80 | 32 | NAD |
| 4 | 83 | 0.38 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3149 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2DT5 · Crystal Structure of TTHA1657 (AT-rich DNA-binding protein) from Thermus thermophilus HB8 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SHS3 · AlphaFold monomer V2.0 prediction for redox-sensing transcriptional repressor rex (Q5SHS3) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q5SHS3
- Elsewhere: RCSB PDB 2DT5 · PDBe 2DT5 · UniProt Q5SHS3
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