Research workbench
S-adenosyl-L-homocysteine hydrolase from bradyrhizobium elkanii in complex with adenosine and cordycepin
Analyse S-adenosyl-L-homocysteine hydrolase from bradyrhizobium elkanii in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M5K
- Type
- protein
- Length
- 1,875 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteinase
- EC
- 3.3.1.1
- UniProt
- A0A087WNH6
- Ligands
- NAD, ADN, 3AD, NA
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 468 | 46% helix, 14% strand | A0A087WNH6 |
| C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 471 | 45% helix, 14% strand | A0A087WNH6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ADN · Adenosine · ligand · 3 copies · chains A, B, C
- 3AD · 3'-deoxyadenosine · ligand · chains D
- NA · Sodium ion · metal · 3 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, D
- PGE · Triethylene glycol · additive · chains C
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.89 | 0.91 | 110 | PEG |
| 2 | 1018 | 0.85 | 0.86 | 108 | NAD, ADN, PEG |
| 3 | 1030 | 0.85 | 0.86 | 111 | NAD, ADN |
| 4 | 1165 | 0.84 | 0.85 | 125 | NAD, ADN |
| 5 | 1183 | 0.82 | 0.83 | 97 | NAD, 3AD |
Interfaces
6 interfaces between chains.
- A–B · 3050 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 2980 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 1793 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1759 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 423 Ų buried · 1 hydrogen bond · protein-protein
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 5M5K · PDBe 5M5K · UniProt A0A087WNH6
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