MolNFT v1 · #11914 · protein
Inhibition of S-adenosylhomocysteine hydrolase by "acyclic sugar" adenosine analogue D-eritadenine
1K0U · S-adenosyl-L-homocysteine hydrolase: “Inhibition of S-adenosylhomocysteine hydrolase by "acyclic sugar" adenosine analogue D-eritadenine”. X-ray diffraction, 2 ligands (NAD, DEA), 20 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 1K0U
- Type
- protein
- Length
- 3,440 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-adenosyl-L-homocysteine hydrolase
- EC
- 3.3.1.1
- UniProt
- P10760
- Ligands
- NAD, DEA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | S-adenosyl-L-homocysteine hydrolase (EC 3.3.1.1) | protein | 430 | 44% helix, 17% strand | P10760 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- DEA · D-eritadenine · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.89 | 0.91 | 79 | empty |
| 2 | 989 | 0.88 | 0.90 | 69 | empty |
| 3 | 643 | 0.86 | 0.91 | 80 | NAD, DEA |
| 4 | 723 | 0.84 | 0.88 | 81 | NAD, DEA |
| 5 | 671 | 0.84 | 0.88 | 85 | NAD, DEA |
Interfaces
14 interfaces between chains.
- G–H · 3257 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 3242 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 3238 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 3222 Ų buried · 35 hydrogen bonds · protein-protein
- E–G · 1888 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1K0U · Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue… · the same entry in another collection · chain H against H, TM-score 1.00
- P10760 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (P10760) · a predicted model of the same protein · 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 P10760
- Elsewhere: RCSB PDB 1K0U · PDBe 1K0U · UniProt P10760
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