MolNFT v1 · #117602 · protein
Crystal structure of human HINT1 complexing with AP5A
5ED3 · Histidine triad nucleotide-binding protein 1: “Crystal structure of human HINT1 complexing with AP5A”. X-ray diffraction, 1 ligand (AMP), 2 pockets (best druggability 0.37). MolNFT v1 #117602 on GenesisL1: 3D structure, binding…
- PDB
- 5ED3
- 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
- AMP
- 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 | 113 | 29% helix, 25% strand | P49773 |
| B | Histidine triad nucleotide-binding protein 1 (EC 3.-.-.-) | protein | 115 | 29% helix, 24% strand | P49773 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
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 | 98 | 0.37 | 0.75 | 23 | AMP |
| 2 | 85 | 0.33 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2008 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 5ED3 · crystal structure of human Hint1 complexing with AP5A · 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 5ED3 · PDBe 5ED3 · UniProt P49773
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