MolNFT v1 · #124680 · protein
Human histidine triad nucleotide binding protein 2 (HHINT2) adenosine complex
5KM9 · Histidine triad nucleotide-binding protein 2, mitochondrial: “Human histidine triad nucleotide binding protein 2 (HHINT2) adenosine complex”. X-ray diffraction, 2 ligands (ADN, CL), 1 pocket (best druggability 0.34). MolNFT v1…
- PDB
- 5KM9
- Type
- protein
- Length
- 213 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine triad nucleotide-binding protein 2, mitochondrial
- EC
- 3.-.-.-
- UniProt
- Q9BX68
- Ligands
- ADN, CL
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Histidine triad nucleotide-binding protein 2, mitochondrial (EC 3.-.-.-) | protein | 112 | 25% helix, 25% strand | Q9BX68 |
| A | Histidine triad nucleotide-binding protein 2, mitochondrial (EC 3.-.-.-) | protein | 101 | 26% helix, 28% strand | Q9BX68 |
Ligands and binding sites
- ADN · Adenosine · ligand · chains B, A
- CL · Chloride ion · ion · chains A
- PG4 · Tetraethylene glycol · additive · chains B
- GOL · Glycerol · additive · chains B, A
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 | 82 | 0.34 | 0.75 | 23 | ADN, GOL |
Interfaces
1 interface between chains.
- B–A · 2037 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 5KM9 · Human Histidine Triad Nucleotide Binding Protein 2 (hHint2) adenosine complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q9BX68 · AlphaFold monomer V2.0 prediction for histidine triad nucleotide- binding protein 2… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9BX68
- Elsewhere: RCSB PDB 5KM9 · PDBe 5KM9 · UniProt Q9BX68
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