Research workbench
Crystal structure of spermidine synthase from helicobacter pylori
Analyse Crystal structure of spermidine synthase from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CMG
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spermidine synthase
- EC
- 2.5.1.16
- UniProt
- O25503
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spermidine synthase (EC 2.5.1.16) | protein | 262 | 29% helix, 31% strand | O25503 |
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.74 | 0.98 | 26 | empty |
| 2 | 396 | 0.70 | 0.82 | 56 | empty |
| 3 | 330 | 0.68 | 0.82 | 45 | empty |
| 4 | 115 | 0.53 | 0.82 | 23 | empty |
| 5 | 124 | 0.42 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1801 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2CMG · Crystal Structure of Spermidine Synthase from Helicobacter Pylori · the same entry in another collection · chain A against A, TM-score 1.00
- O25503 · AlphaFold monomer V2.0 prediction for polyamine aminopropyltransferase (O25503) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O25503
- Elsewhere: RCSB PDB 2CMG · PDBe 2CMG · UniProt O25503
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