MolNFT v1 · #96614 · protein
Crystal structure of a putative 5'-METHYLTHIOADENOSINE/S- adenosylhomocysteine nucleosidase from francisella philomiragia atcc 25017 (target nysgrc-029335)
4JOS: “Crystal structure of a putative 5'-METHYLTHIOADENOSINE/S- adenosylhomocysteine nucleosidase from francisella…”. X-ray diffraction, 2 ligands (ADE, NA), 3 pockets (best druggability 0.65). MolNFT v1 #96614 on GenesisL1: 3D structure…
- PDB
- 4JOS
- Type
- protein
- Length
- 458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylhomocysteine nucleosidase
- EC
- 3.2.2.9
- UniProt
- B0TZL4
- Ligands
- ADE, NA
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 228 | 38% helix, 30% strand | B0TZL4 |
| B | Adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 230 | 37% helix, 30% strand | B0TZL4 |
Ligands and binding sites
- ADE · Adenine · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
- 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.65 | 0.86 | 32 | ADE |
| 2 | 179 | 0.65 | 0.85 | 33 | ADE |
| 3 | 221 | 0.50 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1764 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4JOS · Crystal structure of a putative 5'-methylthioadenosine/S-adenosylhomocysteine… · 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 B0TZL4
- Elsewhere: RCSB PDB 4JOS · PDBe 4JOS · UniProt B0TZL4
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