MolNFT v1 · #61225 · protein
Crystal structure of E. COLI MTA/SAH nucleosidase in complex with bnt-dadmeimma
3DF9: “Crystal structure of E. COLI MTA/SAH nucleosidase in complex with bnt-dadmeimma”. X-ray diffraction, 1 ligand (DF9), 5 pockets (best druggability 0.72). MolNFT v1 #61225 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DF9
- Type
- protein
- Length
- 466 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
- P0AF14
- Ligands
- DF9
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MTA/SAH nucleosidase (EC 3.2.2.9) | protein | 234 | 38% helix, 32% strand | P0AF14 |
| B | MTA/SAH nucleosidase (EC 3.2.2.9) | protein | 232 | 39% helix, 31% strand | P0AF14 |
Ligands and binding sites
- DF9 · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(benzylsulfanyl)methyl]pyrrolidin-3-ol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.72 | 0.91 | 24 | DF9 |
| 2 | 140 | 0.70 | 0.90 | 24 | DF9 |
| 3 | 319 | 0.64 | 0.80 | 41 | empty |
| 4 | 62 | 0.32 | 0.76 | 17 | empty |
| 5 | 61 | 0.31 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1429 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3DF9 · Crystal structure of E. coli MTA/SAH nucleosidase in complex with BnT-DADMeImmA · the same entry in another collection · chain A against A, TM-score 1.00
- P0AF14 · AlphaFold monomer V2.0 prediction for 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine… · 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 P0AF14
- Elsewhere: RCSB PDB 3DF9 · PDBe 3DF9 · UniProt P0AF14
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