Research workbench
STX2 with adenine
Analyse STX2 with adenine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GA4
- Type
- protein
- Length
- 633 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shiga-like toxin II subunit a; Shiga-like toxin II subunit B
- EC
- 3.2.2.22
- UniProt
- P09385, P09386
- Ligands
- 1PS, ADE, NA
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Shiga-like toxin II subunit a (EC 3.2.2.22) | protein | 283 | 38% helix, 24% strand | P09385 |
| B, C, D, E, F | Shiga-like toxin II subunit B | protein | 70 | 16% helix, 47% strand | P09386 |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 4 copies · chains B, F, C, D, E
- ADE · Adenine · ligand · chains A
- NA · Sodium ion · metal · 5 copies · chains A, C, B, F
- FMT · Formic acid · additive · 5 copies · chains A, C, D, E, F
- EDO · 1,2-ethanediol · additive · chains A, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.73 | 0.80 | 67 | ADE |
| 2 | 142 | 0.44 | 0.76 | 23 | empty |
| 3 | 52 | 0.27 | 0.74 | 19 | empty |
| 4 | 51 | 0.26 | 0.73 | 15 | empty |
Interfaces
10 interfaces between chains.
- E–F · 745 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 741 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 739 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 723 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 692 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2GA4 · Stx2 with adenine · 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 P09385
- Every structure of UniProt P09386
- Elsewhere: RCSB PDB 2GA4 · PDBe 2GA4 · UniProt P09385 · UniProt P09386
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