MolNFT v1 · #61561 · protein
Crystal structure of vibrio cholerae 5'-METHYLTHIOADENOSINE/S-adenosyl homocysteine nucleosidase (mtan) complexed with butylthio-dadme- immucillin a
3DP9 · MTA/SAH nucleosidase: “Crystal structure of vibrio cholerae 5'-METHYLTHIOADENOSINE/S-adenosyl homocysteine nucleosidase (mtan)…”. X-ray diffraction, 2 ligands (BIG, IOD), 4 pockets (best druggability 0.70). MolNFT v1 #61561 on…
- PDB
- 3DP9
- Type
- protein
- Length
- 459 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
- Q9KPI8
- Ligands
- BIG, IOD
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MTA/SAH nucleosidase (EC 3.2.2.9) | protein | 229 | 36% helix, 32% strand | Q9KPI8 |
| C | MTA/SAH nucleosidase (EC 3.2.2.9) | protein | 230 | 37% helix, 32% strand | Q9KPI8 |
Ligands and binding sites
- BIG · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol · ligand · 2 copies · chains A, C
- IOD · Iodide ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.70 | 0.90 | 24 | BIG |
| 2 | 115 | 0.69 | 0.91 | 23 | BIG |
| 3 | 156 | 0.52 | 0.79 | 18 | empty |
| 4 | 52 | 0.24 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–C · 1428 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3DP9 · Crystal structure of Vibrio cholerae 5'-methylthioadenosine/S-adenosyl homocysteine… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KPI8 · 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 Q9KPI8
- Elsewhere: RCSB PDB 3DP9 · PDBe 3DP9 · UniProt Q9KPI8
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