Research workbench
Crystal structure of E. COLI AMP nucleosidase
Analyse Crystal structure of E. COLI AMP nucleosidase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T8R
- Type
- protein
- Length
- 2,778 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
- 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 | 463 | 41% helix, 21% strand | P15272 |
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 | 649 | 0.88 | 0.93 | 83 | empty |
| 2 | 537 | 0.85 | 0.91 | 62 | empty |
| 3 | 513 | 0.84 | 0.91 | 58 | empty |
| 4 | 652 | 0.80 | 0.84 | 91 | empty |
| 5 | 694 | 0.79 | 0.83 | 77 | empty |
Interfaces
9 interfaces between chains.
- E–F · 2932 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 2907 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2889 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 2203 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 2152 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 1T8R · Crystal Structure of E. coli AMP Nucleosidase · 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 1T8R · PDBe 1T8R · UniProt P15272
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