Research workbench
Crystal structure of E.COLI AMP nucleosidase complexed with phosphate
Analyse Crystal structure of E.COLI AMP nucleosidase complexed with phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T8Y
- Type
- protein
- Length
- 2,766 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
- PO4
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | AMP nucleosidase (EC 3.2.2.4) | protein | 461 | 41% helix, 21% strand | P15272 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, F, B, C, D, E
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 | 684 | 0.88 | 0.93 | 81 | empty |
| 2 | 731 | 0.88 | 0.92 | 81 | empty |
| 3 | 1173 | 0.87 | 0.88 | 131 | empty |
| 4 | 655 | 0.77 | 0.83 | 75 | PO4 |
| 5 | 575 | 0.77 | 0.83 | 75 | PO4 |
Interfaces
12 interfaces between chains.
- A–B · 2848 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2829 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 2797 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 2247 Ų buried · 30 hydrogen bonds · protein-protein
- D–E · 2223 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1T8Y · Crystal Structure of E.coli AMP Nucleosidase complexed with phosphate · 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 1T8Y · PDBe 1T8Y · UniProt P15272
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