Research workbench
Crystal structure of the E352T mutant of S-adenosyl-L-homocysteine hydrolase from synechocystis sp. pcc 6803 cocrystallized with adenosine in the presence of rb+ cations
Analyse Crystal structure of the E352T mutant of S-adenosyl-L-homocysteine hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ZD9
- Type
- protein
- Length
- 834 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- P74008
- Ligands
- NAD, ADN, RB, CL
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 417 | 49% helix, 17% strand | P74008 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, C
- ADN · Adenosine · ligand · 2 copies · chains A, C
- RB · Rubidium ion · metal · 3 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.73 | 0.85 | 48 | NAD, ADN |
| 2 | 317 | 0.72 | 0.85 | 52 | NAD, ADN |
| 3 | 368 | 0.65 | 0.80 | 44 | empty |
| 4 | 348 | 0.64 | 0.79 | 46 | empty |
| 5 | 459 | 0.61 | 0.76 | 42 | empty |
Interfaces
1 interface between chains.
- A–C · 1765 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7ZD9 · Crystal structure of the E352T mutant of S-adenosyl-L-homocysteine hydrolase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P74008 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (P74008) · 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 P74008
- Elsewhere: RCSB PDB 7ZD9 · PDBe 7ZD9 · UniProt P74008
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