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Crystal structure of brucella melitensis 5'-METHYLTHIOADENOSINE/S- adenosylhomocysteine nucleosidase
Analyse Crystal structure of brucella melitensis 5'-METHYLTHIOADENOSINE/S… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PR3
- Type
- protein
- Length
- 404 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-methylthioadenosine nucleosidase / S- adenosylhomocysteine nucleosidase
- EC
- 3.2.2.16, 3.2.2.9
- UniProt
- Q8YBL1
- Ligands
- ADE, PO4
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-methylthioadenosine nucleosidase / S- adenosylhomocysteine nucleosidase (EC 3.2.2.16, 3.2.2.9) | protein | 205 | 28% helix, 26% strand | Q8YBL1 |
| B | 5'-methylthioadenosine nucleosidase / S- adenosylhomocysteine nucleosidase (EC 3.2.2.16, 3.2.2.9) | protein | 199 | 31% helix, 28% strand | Q8YBL1 |
Ligands and binding sites
- ADE · Adenine · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains 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 | 260 | 0.69 | 0.84 | 34 | ADE |
| 2 | 200 | 0.61 | 0.82 | 27 | ADE |
| 3 | 384 | 0.60 | 0.77 | 44 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1390 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 4PR3 · Crystal structure of Brucella melitensis 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 Q8YBL1
- Elsewhere: RCSB PDB 4PR3 · PDBe 4PR3 · UniProt Q8YBL1
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