MolNFT v1 · #111292 · protein
Crystal structure of escherichia COLI 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan) complexed with (3S,4R)- methylthio-dadme-immucillin-a
4YML · 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase: “Crystal structure of escherichia COLI 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan)…”. X-ray diffraction, 2 ligands (4F0, PO4), 1 pocket (best…
- PDB
- 4YML
- Type
- protein
- Length
- 231 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase
- EC
- 3.2.2.9
- UniProt
- P0AF12
- Ligands
- 4F0, PO4
- Pockets
- 1 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 231 | 39% helix, 30% strand | P0AF12 |
Ligands and binding sites
- 4F0 · (3S,4R)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(methylsulfanyl)methyl]pyrrolidin-3-ol · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.62 | 0.88 | 19 | 4F0 |
Compared structures
- 4YML · Crystal structure of Escherichia coli 5'-methylthioadenosine/S-adenosyl homocysteine… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AF12 · AlphaFold monomer V2.0 prediction for 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine… · a predicted model of the same protein · 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 P0AF12
- Elsewhere: RCSB PDB 4YML · PDBe 4YML · UniProt P0AF12
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