Research workbench
Crystal structure of GD2 bound pltb
Analyse Crystal structure of GD2 bound pltb in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RHS
- Type
- protein
- Length
- 571 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative pertussis-like toxin subunit
- UniProt
- Q8Z6A3
- Ligands
- SIA, GAL
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Putative pertussis-like toxin subunit | protein | 114 | 20% helix, 42% strand | Q8Z6A3 |
| B | Putative pertussis-like toxin subunit | protein | 115 | 20% helix, 42% strand | Q8Z6A3 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains C, E
- GAL · beta-D-galactopyranose · sugar · 2 copies
- ACT · Acetate ion · additive · 2 copies · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 852 | 0.71 | 0.76 | 36 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1099 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1077 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1072 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1065 Ų buried · 24 hydrogen bonds · protein-protein
- B–E · 1058 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4RHS · Crystal structure of GD2 bound PltB · 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 Q8Z6A3
- Elsewhere: RCSB PDB 4RHS · PDBe 4RHS · UniProt Q8Z6A3
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