Research workbench
Apo form of AB5 holotoxin
Analyse Apo form of AB5 holotoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L63
- Type
- protein
- Length
- 771 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ecxa; Ecxb
- EC
- 3.4.24.-
- UniProt
- Q8GAV4, Q8GAV3
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ecxa (EC 3.4.24.-) | protein | 249 | 35% helix, 20% strand | Q8GAV4 |
| B, C, D | Ecxb | protein | 105 | 24% helix, 38% strand | Q8GAV3 |
| E | Ecxb | protein | 104 | 24% helix, 36% strand | Q8GAV3 |
| F | Ecxb | protein | 103 | 24% helix, 37% strand | Q8GAV3 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 5 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.82 | 0.84 | 73 | empty |
| 2 | 333 | 0.61 | 0.78 | 37 | ZN |
| 3 | 379 | 0.61 | 0.77 | 49 | empty |
| 4 | 300 | 0.54 | 0.75 | 36 | empty |
| 5 | 96 | 0.50 | 0.83 | 26 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1350 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 1347 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1341 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1341 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1308 Ų buried · 29 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4L63 · Apo form of AB5 holotoxin · 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 Q8GAV4
- Every structure of UniProt Q8GAV3
- Elsewhere: RCSB PDB 4L63 · PDBe 4L63 · UniProt Q8GAV4 · UniProt Q8GAV3
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