MolNFT v1 · #153187 · protein
Crystal structure of human HINT1 mutant complexing with AP4A II
6J65 · Histidine triad nucleotide-binding protein 1: “Crystal structure of human HINT1 mutant complexing with AP4A II”. X-ray diffraction, 1 ligand (B4P), 6 pockets (best druggability 0.57). MolNFT v1 #153187 on GenesisL1: 3D structure…
- PDB
- 6J65
- Type
- protein
- Length
- 452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histidine triad nucleotide-binding protein 1
- EC
- 3.-.-.-
- UniProt
- P49773
- Ligands
- B4P
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Histidine triad nucleotide-binding protein 1 (EC 3.-.-.-) | protein | 111 | 30% helix, 25% strand | P49773 |
| B, E | Histidine triad nucleotide-binding protein 1 (EC 3.-.-.-) | protein | 115 | 29% helix, 24% strand | P49773 |
Ligands and binding sites
- B4P · Bis(adenosine)-5'-tetraphosphate · ligand · chains A, B, E
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.57 | 0.77 | 36 | B4P, EPE |
| 2 | 161 | 0.47 | 0.76 | 33 | empty |
| 3 | 81 | 0.40 | 0.78 | 24 | empty |
| 4 | 78 | 0.40 | 0.78 | 23 | empty |
| 5 | 83 | 0.32 | 0.73 | 22 | empty |
Interfaces
3 interfaces between chains.
- D–E · 1993 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 1967 Ų buried · 40 hydrogen bonds · protein-protein
- B–E · 460 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6J65 · Crystal structure of human HINT1 mutant complexing with AP4A II · 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 6J65 · PDBe 6J65 · UniProt P49773
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