Research workbench
Crystal structure of E.COLI AMP nucleosidase complexed with formicin 5'-monophosphate
Analyse Crystal structure of E.COLI AMP nucleosidase complexed with formicin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T8S
- Type
- protein
- Length
- 2,659 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMP nucleosidase
- EC
- 3.2.2.4
- UniProt
- P15272
- Ligands
- FMP
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | AMP nucleosidase (EC 3.2.2.4) | protein | 443 | 40% helix, 21% strand | P15272 |
| B | AMP nucleosidase (EC 3.2.2.4) | protein | 444 | 40% helix, 21% strand | P15272 |
Ligands and binding sites
- FMP · Formycin-5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.84 | 0.86 | 101 | FMP |
| 2 | 827 | 0.84 | 0.86 | 86 | FMP |
| 3 | 1030 | 0.84 | 0.85 | 114 | FMP |
| 4 | 684 | 0.79 | 0.84 | 77 | empty |
| 5 | 677 | 0.77 | 0.82 | 67 | empty |
Interfaces
8 interfaces between chains.
- B–C · 2149 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 2143 Ų buried · 22 hydrogen bonds · protein-protein
- A–F · 2110 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1959 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1851 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1T8S · Crystal Structure of E.coli AMP Nucleosidase complexed with formicin 5'-monophosphate · 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 P15272
- Elsewhere: RCSB PDB 1T8S · PDBe 1T8S · UniProt P15272
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