Research workbench
Crystal structure of E. coli MTA/AdoHcy nucleosidase complexed with formycin A (FMA)
Analyse Crystal structure of E. coli MTA/AdoHcy nucleosidase complexed with formycin A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NC3
- Type
- protein
- Length
- 465 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Escherichia coli
- Molecule
- MTA/SAH nucleosidase
- EC
- 3.2.2.9
- UniProt
- P24247
- Ligands
- FMC
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.2 · 2 distinct chains · 38% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MTA/SAH nucleosidase (EC 3.2.2.9) | protein | 235 | 38% helix, 31% strand | P24247 |
| B | MTA/SAH nucleosidase (EC 3.2.2.9) | protein | 230 | 38% helix, 32% strand | P24247 |
Ligands and binding sites
- FMC · (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol · 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 | 153 | 0.74 | 0.92 | 34 | FMC |
| 2 | 112 | 0.70 | 0.91 | 25 | FMC |
| 3 | 286 | 0.63 | 0.81 | 38 | empty |
| 4 | 58 | 0.32 | 0.76 | 18 | empty |
| 5 | 68 | 0.32 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1416 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 1NC3 · Crystal structure of E. COLI MTA/ADOHCY nucleosidase complexed with formycin a (fma) · 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 P24247
- Elsewhere: RCSB PDB 1NC3 · PDBe 1NC3 · UniProt P24247
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