Research workbench
Human histidine triad nucleotide binding protein 1 (HHINT1) nucleoside thiophosphoramidate covalent intermediate complex
Analyse Human histidine triad nucleotide binding protein 1 (HHINT1) nucleoside… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IPD
- Type
- protein
- Length
- 228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine triad nucleotide-binding protein 1
- EC
- 3.-.-.-
- UniProt
- P49773
- Ligands
- 6CG
- Pockets
- 2 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histidine triad nucleotide-binding protein 1 (EC 3.-.-.-) | protein | 115 | 29% helix, 24% strand | P49773 |
| B | Histidine triad nucleotide-binding protein 1 (EC 3.-.-.-) | protein | 113 | 29% helix, 25% strand | P49773 |
Ligands and binding sites
- 6CG · 5'-S-phosphono-5'-thioguanosine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.37 | 0.75 | 23 | 6CG |
| 2 | 69 | 0.32 | 0.74 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 2023 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5IPD · Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) nucleoside… · the same entry in another collection · chain A 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 P49773
- Elsewhere: RCSB PDB 5IPD · PDBe 5IPD · UniProt P49773
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