Research workbench
Crystal structure of S-adenosyl-L-homocysteine hydrolase from bradyrhizobium elkanii in complex with adenine
Analyse Crystal structure of S-adenosyl-L-homocysteine hydrolase from bradyrhizobium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M65
- Type
- protein
- Length
- 937 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- A0A087WNH6
- Ligands
- NAD, ADE, NA, BR
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 469 | 47% helix, 14% strand | A0A087WNH6 |
| B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 468 | 47% helix, 14% strand | A0A087WNH6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ADE · Adenine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- BR · Bromide ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 5 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.85 | 0.88 | 92 | EDO, NAD, ADE |
| 2 | 904 | 0.85 | 0.87 | 110 | NAD, ADE |
| 3 | 463 | 0.79 | 0.86 | 30 | empty |
| 4 | 65 | 0.40 | 0.80 | 13 | empty |
| 5 | 54 | 0.28 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 3100 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 5M65 · Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A087WNH6
- Elsewhere: RCSB PDB 5M65 · PDBe 5M65 · UniProt A0A087WNH6
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