Research workbench
Crystal structure of S-adenosyl-L-homocysteine hydrolase from burkholderia pseudomallei
Analyse Crystal structure of S-adenosyl-L-homocysteine hydrolase from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D64
- Type
- protein
- Length
- 924 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- Q3JY79
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 462 | 45% helix, 14% strand | Q3JY79 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.80 | 0.90 | 31 | empty |
| 2 | 1171 | 0.79 | 0.81 | 97 | NAD |
| 3 | 991 | 0.77 | 0.79 | 81 | NAD |
| 4 | 145 | 0.44 | 0.76 | 28 | empty |
| 5 | 84 | 0.37 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2792 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3D64 · Crystal structure of S-adenosyl-L-homocysteine hydrolase from Burkholderia pseudomallei · the same entry in another collection · chain A against A, TM-score 1.00
- Q3JY79 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (Q3JY79) · a predicted model of the same protein · chain A against A, TM-score 0.85
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 Q3JY79
- Elsewhere: RCSB PDB 3D64 · PDBe 3D64 · UniProt Q3JY79
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