MolNFT v1 · #138391 · protein
Crystal structure of 3'SL bound pltb
5WHT · Putative pertussis-like toxin subunit: “Crystal structure of 3'SL bound pltb”. X-ray diffraction, 3 ligands (SIA, GAL, GLC), 1 pocket (best druggability 0.69). MolNFT v1 #138391 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5WHT
- Type
- protein
- Length
- 573 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, GLC
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative pertussis-like toxin subunit | protein | 115 | 20% helix, 40% strand | Q8Z6A3 |
| D, E | Putative pertussis-like toxin subunit | protein | 114 | 20% helix, 42% strand | Q8Z6A3 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 4 copies · chains A, C, B, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
- GLC · alpha-D-glucopyranose · sugar
- ACT · Acetate ion · additive · 8 copies · chains A, B, E, C, D
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains B, D, 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 | 779 | 0.69 | 0.76 | 33 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1079 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1077 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 1065 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1030 Ų buried · 26 hydrogen bonds · protein-protein
- B–E · 1024 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5WHT · Crystal structure of 3'SL 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 5WHT · PDBe 5WHT · UniProt Q8Z6A3
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