Research workbench
Crystal structure of the STX2A complexed with rra peptide
Analyse Crystal structure of the STX2A complexed with rra peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VHF
- Type
- protein
- Length
- 633 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA N-glycosylase; Shiga toxin 2 B subunit; Rra peptide
- EC
- 3.2.2.22
- UniProt
- Q8XBV2, Q7DJJ2
- Ligands
- 1PS, NH2
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RRNA N-glycosylase (EC 3.2.2.22) | protein | 283 | 39% helix, 24% strand | Q8XBV2 |
| B | Shiga toxin 2 B subunit | protein | 67 | 16% helix, 48% strand | Q7DJJ2 |
| C, D, E, F | Shiga toxin 2 B subunit | protein | 70 | 16% helix, 49% strand | Q7DJJ2 |
| G | Rra peptide | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 4 copies · chains B, C, D, E, F
- NH2 · Amino group · ion · chains A, G
- GOL · Glycerol · additive · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.64 | 0.80 | 36 | empty |
| 2 | 238 | 0.53 | 0.76 | 34 | empty |
| 3 | 155 | 0.45 | 0.76 | 31 | empty |
Interfaces
12 interfaces between chains.
- E–F · 749 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 745 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 743 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 729 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 688 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7VHF · Crystal structure of the STX2a complexed with RRA peptide · 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 Q8XBV2
- Every structure of UniProt Q7DJJ2
- Elsewhere: RCSB PDB 7VHF · PDBe 7VHF · UniProt Q8XBV2 · UniProt Q7DJJ2
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