Research workbench
Native structure of futalosine hydrolase of helicobacter pylori strain 26695
Analyse Native structure of futalosine hydrolase of helicobacter pylori strain 26695 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BMX
- Type
- protein
- Length
- 458 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MTA/SAH nucleosidase
- EC
- 3.2.2.9
- UniProt
- O24915
- Ligands
- ADE
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MTA/SAH nucleosidase (EC 3.2.2.9) | protein | 225 | 38% helix, 31% strand | O24915 |
| B | MTA/SAH nucleosidase (EC 3.2.2.9) | protein | 233 | 36% helix, 30% strand | O24915 |
Ligands and binding sites
- ADE · Adenine · ligand · chains B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.68 | 0.90 | 26 | ADE, TRS |
| 2 | 258 | 0.64 | 0.81 | 26 | empty |
| 3 | 175 | 0.45 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1642 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4BMX · Native structure of futalosine hydrolase of Helicobacter pylori strain 26695 · the same entry in another collection · chain A against A, TM-score 1.00
- O24915 · AlphaFold monomer V2.0 prediction for aminodeoxyfutalosine nucleosidase (O24915) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O24915
- Elsewhere: RCSB PDB 4BMX · PDBe 4BMX · UniProt O24915
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