MolNFT v1 · #62405 · protein
Crystal structure of 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase from neisseria meningitidis in complex with methylthio- immucillin-a
3EEI · 5-methylthioadenosine NUCLEOSIDASE/S-adenosylhomocysteine…: “Crystal structure of 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase from neisseria meningitidis…”. X-ray diffraction, 1 ligand (MTM), 4 pockets (best…
- PDB
- 3EEI
- Type
- protein
- Length
- 462 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
- Q9K054
- Ligands
- MTM
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5-methylthioadenosine NUCLEOSIDASE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.16, 3.2.2.9) | protein | 231 | 37% helix, 31% strand | Q9K054 |
Ligands and binding sites
- MTM · (3S,4R)-2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-[(methylsulfanyl)methyl]pyrrolidine-3,4-diol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.71 | 0.92 | 24 | MTM |
| 2 | 162 | 0.69 | 0.88 | 35 | MTM |
| 3 | 163 | 0.47 | 0.77 | 28 | empty |
| 4 | 90 | 0.37 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1870 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3EEI · Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from… · 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 Q9K054
- Elsewhere: RCSB PDB 3EEI · PDBe 3EEI · UniProt Q9K054
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