Research workbench
Crystal structure of the inactive form of S-adenosyl-L-homocysteine hydrolase from thermotoga maritima in ternary complex with NADH and adenosine
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
- 5TOW
- Type
- protein
- Length
- 791 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
- ADN, NAI, CL
- Pockets
- 7 · best druggability 0.83
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 | 388 | 45% helix, 17% strand | O51933 |
| B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 403 | 45% helix, 16% strand | O51933 |
Ligands and binding sites
- ADN · Adenosine · ligand · chains A
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · chains B
- CL · Chloride ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.83 | 0.84 | 97 | NAI |
| 2 | 471 | 0.69 | 0.80 | 70 | empty |
| 3 | 227 | 0.50 | 0.75 | 36 | MPD |
| 4 | 244 | 0.50 | 0.75 | 27 | empty |
| 5 | 159 | 0.47 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1423 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5TOW · Crystal structure of the inactive form of S-adenosyl-L-homocysteine hydrolase from… · the same entry in another collection · chain B against B, 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 5TOW · PDBe 5TOW · UniProt O51933
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