Research workbench
A thermophilic S-adenosylhomocysteine hydrolase
Analyse A thermophilic S-adenosylhomocysteine hydrolase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3X2F
- Type
- protein
- Length
- 810 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- O51933
- Ligands
- NAI, NA, NO3
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 406 | 45% helix, 17% strand | O51933 |
| B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 404 | 47% helix, 16% strand | O51933 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 3 copies · chains A, B
- NO3 · Nitrate ion · ion · 40 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1198 | 0.79 | 0.81 | 145 | NAI, NO3 |
| 2 | 412 | 0.76 | 0.85 | 56 | NAI, NO3 |
| 3 | 62 | 0.73 | 0.99 | 19 | empty |
| 4 | 202 | 0.58 | 0.80 | 27 | NO3 |
| 5 | 271 | 0.53 | 0.75 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 1659 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
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 O51933
- Elsewhere: RCSB PDB 3X2F · PDBe 3X2F · UniProt O51933
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