Research workbench
Pertussis toxin E129D NAD
Analyse Pertussis toxin E129D NAD in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U6Z
- Type
- protein
- Length
- 336 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pertussis toxin subunit 1
- EC
- 2.4.2.-, 2.4.2.30
- UniProt
- P04977
- Ligands
- NAD, IOD
- Pockets
- 4 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Pertussis toxin subunit 1 (EC 2.4.2.-, 2.4.2.30) | protein | 167 | 28% helix, 31% strand | P04977 |
| A | Pertussis toxin subunit 1 (EC 2.4.2.-, 2.4.2.30) | protein | 169 | 28% helix, 30% strand | P04977 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains B, A
- IOD · Iodide ion · ion · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.66 | 0.81 | 40 | empty |
| 2 | 260 | 0.60 | 0.79 | 31 | IOD, NAD |
| 3 | 264 | 0.57 | 0.78 | 31 | IOD, NAD |
| 4 | 66 | 0.30 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- B–A · 408 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
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 P04977
- Elsewhere: RCSB PDB 7U6Z · PDBe 7U6Z · UniProt P04977
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