MolNFT v1 · #189476 · protein
Crystal structure of the STX2A complexed with rrra peptide
7VHE · RRNA N-glycosylase: “Crystal structure of the STX2A complexed with rrra peptide”. X-ray diffraction, 2 ligands (1PS, NH2), 3 pockets (best druggability 0.63). MolNFT v1 #189476 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7VHE
- Type
- protein
- Length
- 634 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RRNA N-glycosylase; Shiga toxin 2 B subunit; Rrra peptide
- EC
- 3.2.2.22
- UniProt
- Q8XBV2, Q7DJJ2
- Ligands
- 1PS, NH2
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 31% 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, 44% strand | Q7DJJ2 |
| G | Rrra peptide | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- 1PS · 3-pyridinium-1-ylpropane-1-sulfonate · ligand · 4 copies · chains B, C, D, 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 | 221 | 0.63 | 0.83 | 32 | empty |
| 2 | 305 | 0.55 | 0.76 | 39 | empty |
| 3 | 134 | 0.43 | 0.76 | 26 | empty |
Interfaces
12 interfaces between chains.
- E–F · 758 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 737 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 735 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 727 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 687 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7VHE · Crystal structure of the STX2a complexed with RRRA 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 7VHE · PDBe 7VHE · UniProt Q8XBV2 · UniProt Q7DJJ2
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