Research workbench
Crystal structure of lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with cordycepin
Analyse Crystal structure of lupinus luteus S-adenosyl-L-homocysteine hydrolase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ONF
- Type
- protein
- Length
- 973 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- Q9SP37
- Ligands
- NAD, 3AD, NA
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 485 | 46% helix, 15% strand | Q9SP37 |
| B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 488 | 47% helix, 15% strand | Q9SP37 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- 3AD · 3'-deoxyadenosine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.86 | 0.88 | 124 | NAD, 3AD |
| 2 | 737 | 0.86 | 0.89 | 97 | NAD, 3AD |
| 3 | 423 | 0.80 | 0.88 | 32 | empty |
| 4 | 80 | 0.41 | 0.79 | 17 | empty |
| 5 | 63 | 0.28 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 3160 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3ONF · Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9SP37 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (Q9SP37) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9SP37
- Elsewhere: RCSB PDB 3ONF · PDBe 3ONF · UniProt Q9SP37
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