MolNFT v1 · #183868 · protein
Crystal structure of S-adenosyl-L-homocysteine hydrolase from synechocystis sp. pcc 6803 cocrystallized with adenosine in the presence of rb+ cations
7O5L · Adenosylhomocysteinase: “Crystal structure of S-adenosyl-L-homocysteine hydrolase from synechocystis sp. pcc 6803 cocrystallized with…”. X-ray diffraction, 4 ligands (NAD, ADN, RB), 8 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 7O5L
- Type
- protein
- Length
- 830 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 0.74
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 417 | 49% helix, 17% strand | P74008 |
| C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 413 | 48% 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 · 5 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, 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 | 483 | 0.74 | 0.83 | 71 | NAD, ADN |
| 2 | 316 | 0.71 | 0.84 | 52 | NAD, ADN |
| 3 | 322 | 0.65 | 0.80 | 42 | empty |
| 4 | 313 | 0.63 | 0.79 | 36 | empty |
| 5 | 397 | 0.58 | 0.75 | 38 | RB |
Interfaces
1 interface between chains.
- A–C · 1727 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 7O5L · Crystal structure of S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803… · 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 C 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 7O5L · PDBe 7O5L · UniProt P74008
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