Research workbench
Crystal structure of the inactive form of S-adenosyl-L-homocysteine hydrolase from thermotoga maritima in binary complex with NADH
Analyse Crystal structure of the inactive form 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
- 5TOV
- Type
- protein
- Length
- 785 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, CL
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 382 | 45% helix, 17% strand | O51933 |
| B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 403 | 45% helix, 16% strand | O51933 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 938 | 0.85 | 0.86 | 85 | NAI |
| 2 | 272 | 0.57 | 0.77 | 40 | empty |
| 3 | 62 | 0.45 | 0.83 | 20 | empty |
| 4 | 191 | 0.44 | 0.74 | 24 | empty |
| 5 | 55 | 0.43 | 0.83 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1393 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5TOV · Crystal structure of the inactive form of S-adenosyl-L-homocysteine hydrolase from… · the same entry in another collection · chain A against A, TM-score 1.00
- O51933 · AlphaFold monomer V2.0 prediction for adenosylhomocysteinase (O51933) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 5TOV · PDBe 5TOV · UniProt O51933
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