MolNFT v1 · #73536 · protein
Crystal structure of E. COLI MTA/SAH nucleosidase in complex with (4- CHLOROPHENYL)THIO-dadme-imma
3O4V: “Crystal structure of E. COLI MTA/SAH nucleosidase in complex with (4- CHLOROPHENYL)THIO-dadme-imma”. X-ray diffraction, 1 ligand (4CT), 4 pockets (best druggability 0.71). MolNFT v1 #73536 on GenesisL1: 3D structure, binding sites…
- PDB
- 3O4V
- 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, 3.2.2.16
- UniProt
- D3QWG1
- Ligands
- 4CT
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MTA/SAH nucleosidase (EC 3.2.2.9, 3.2.2.16) | protein | 234 | 38% helix, 32% strand | D3QWG1 |
| B | MTA/SAH nucleosidase (EC 3.2.2.9, 3.2.2.16) | protein | 232 | 39% helix, 32% strand | D3QWG1 |
Ligands and binding sites
- 4CT · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-{[(4-chlorophenyl) sulfanyl]methyl}pyrrolidin-3-ol · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- IPA · Isopropyl alcohol · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.71 | 0.90 | 23 | 4CT |
| 2 | 139 | 0.71 | 0.90 | 23 | 4CT |
| 3 | 311 | 0.63 | 0.80 | 37 | GOL |
| 4 | 56 | 0.31 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1441 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3O4V · Crystal structure of E. coli MTA/SAH nucleosidase in complex with… · 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 D3QWG1
- Elsewhere: RCSB PDB 3O4V · PDBe 3O4V · UniProt D3QWG1
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