MolNFT v1 · #126549 · protein
Crystal structure of S-adenosyl-L-homocysteine hydrolase from bradyrhizobium elkanii in complex with adenine and 2'-deoxyadenosine
5M67 · Adenosylhomocysteinase: “Crystal structure of S-adenosyl-L-homocysteine hydrolase from bradyrhizobium elkanii in complex with adenine…”. X-ray diffraction, 4 ligands (NAD, ADE, 3D1), 19 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 5M67
- Type
- protein
- Length
- 1,869 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, ADE, 3D1, NA
- Pockets
- 19 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 468 | 46% helix, 14% strand | A0A087WNH6 |
| B | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 463 | 48% helix, 14% strand | A0A087WNH6 |
| D | Adenosylhomocysteinase (EC 3.3.1.1) | protein | 470 | 45% helix, 14% strand | A0A087WNH6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- ADE · Adenine · ligand · 2 copies · chains A, B
- 3D1 · (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol · ligand · 2 copies · chains C, D
- NA · Sodium ion · metal · 5 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, C, B, D
- ACT · Acetate ion · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 964 | 0.89 | 0.91 | 87 | NA, PEG |
| 2 | 1118 | 0.83 | 0.84 | 111 | NAD, 3D1 |
| 3 | 1047 | 0.82 | 0.83 | 107 | NAD, ADE, ACT |
| 4 | 1155 | 0.82 | 0.83 | 111 | NAD, 3D1, ACT |
| 5 | 1165 | 0.82 | 0.83 | 120 | NAD, ADE |
Interfaces
6 interfaces between chains.
- C–D · 3196 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 3138 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 1810 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1791 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 434 Ų buried · 5 hydrogen bonds · 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 5M67 · PDBe 5M67 · UniProt A0A087WNH6
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