MolNFT v1 · #27239 · protein
Complex of diphtheria toxin and heparin-binding epidermal growth factor
1XDT: “Complex of diphtheria toxin and heparin-binding epidermal growth factor”. X-ray diffraction, 3 pockets (best druggability 0.47). MolNFT v1 #27239 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1XDT
- Type
- protein
- Length
- 559 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diphtheria toxin; Heparin-binding epidermal growth factor
- EC
- 2.4.2.36
- UniProt
- P00588, Q99075
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| T | Diphtheria toxin (EC 2.4.2.36) | protein | 518 | 36% helix, 27% strand | P00588 |
| R | Heparin-binding epidermal growth factor | protein | 41 | 7% helix, 29% strand | Q99075 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.47 | 0.75 | 23 | empty |
| 2 | 70 | 0.38 | 0.78 | 17 | empty |
| 3 | 75 | 0.30 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- T–R · 1132 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1XDT · Complex of diphtheria toxin and heparin-binding epidermal growth factor · the same entry in another collection · chain T against T, TM-score 1.00
- Q99075 · AlphaFold monomer V2.0 prediction for proheparin-binding EGF-like growth factor (Q99075) · a predicted model of the same protein · chain R against A, TM-score 0.92
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 P00588
- Every structure of UniProt Q99075
- Elsewhere: RCSB PDB 1XDT · PDBe 1XDT · UniProt P00588 · UniProt Q99075
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