Research workbench
Crystal structure of S-adenosyl-L-homocysteine hydrolase from pseudomonas aeruginosa in complex with 3'-deoxyadenosine and K+ cation
Analyse Crystal structure of S-adenosyl-L-homocysteine hydrolase from pseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6F3P
- Type
- protein
- Length
- 920 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- Q9I685
- Ligands
- NAD, 3AD, K, CL, PO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 460 | 46% helix, 15% strand | Q9I685 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, C
- 3AD · 3'-deoxyadenosine · ligand · 2 copies · chains A, C
- K · Potassium ion · metal · 2 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.73 | 0.85 | 58 | NAD, 3AD, CL |
| 2 | 384 | 0.73 | 0.84 | 55 | NAD, 3AD, CL |
| 3 | 52 | 0.68 | 0.97 | 19 | empty |
| 4 | 577 | 0.65 | 0.76 | 40 | empty |
| 5 | 275 | 0.53 | 0.75 | 29 | empty |
Interfaces
1 interface between chains.
- A–C · 1912 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6F3P · Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I685 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (Q9I685) · 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 Q9I685
- Elsewhere: RCSB PDB 6F3P · PDBe 6F3P · UniProt Q9I685
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