Research workbench
Crystal structure of aminotransferase aspb (NP_207418.1) from helicobacter pylori 26695 at 2.19 a resolution
Analyse Crystal structure of aminotransferase aspb (NP_207418.1) from helicobacter… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EZS
- Type
- protein
- Length
- 748 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminotransferase aspb
- UniProt
- O25341
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aminotransferase aspb | protein | 374 | 44% helix, 14% strand | O25341 |
| B | Aminotransferase aspb | protein | 374 | 46% helix, 14% strand | O25341 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 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 | 600 | 0.76 | 0.83 | 63 | PO4, EDO |
| 2 | 558 | 0.72 | 0.80 | 62 | PO4 |
| 3 | 110 | 0.51 | 0.81 | 19 | empty |
| 4 | 59 | 0.34 | 0.77 | 16 | empty |
| 5 | 67 | 0.33 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2491 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 3EZS · Crystal structure of aminotransferase AspB (NP_207418.1) from HELICOBACTER PYLORI 26695… · 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 O25341
- Elsewhere: RCSB PDB 3EZS · PDBe 3EZS · UniProt O25341
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