MolNFT v1 · #21971 · protein
Crystal structure of the haemophilus ducreyi cytolethal distending toxin
1SR4 · Cytolethal distending toxin subunit a: “Crystal structure of the haemophilus ducreyi cytolethal distending toxin”. X-ray diffraction, 1 ligand (BR), 8 pockets (best druggability 0.64). MolNFT v1 #21971 on GenesisL1: 3D structure…
- PDB
- 1SR4
- Type
- protein
- Length
- 579 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytolethal distending toxin subunit a; Cytolethal distending toxin protein B; Cytolethal…
- UniProt
- O06522, O06523, O06524
- Ligands
- BR
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytolethal distending toxin subunit a | protein | 167 | 10% helix, 43% strand | O06522 |
| B | Cytolethal distending toxin protein B | protein | 258 | 20% helix, 29% strand | O06523 |
| C | Cytolethal distending toxin protein C | protein | 154 | 7% helix, 31% strand | O06524 |
Ligands and binding sites
- BR · Bromide ion · ion · 26 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.64 | 0.86 | 30 | BR |
| 2 | 134 | 0.59 | 0.85 | 32 | BR |
| 3 | 240 | 0.51 | 0.75 | 35 | BR |
| 4 | 120 | 0.43 | 0.77 | 21 | empty |
| 5 | 96 | 0.38 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1575 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1515 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1424 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1SR4 · Crystal Structure of the Haemophilus ducreyi cytolethal distending toxin · the same entry in another collection · chain A against A, TM-score 1.00
- O06522 · AlphaFold monomer V2.0 prediction for cytolethal distending toxin subunit a (O06522) · a predicted model of the same protein · 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 O06522
- Every structure of UniProt O06523
- Every structure of UniProt O06524
- Elsewhere: RCSB PDB 1SR4 · PDBe 1SR4 · UniProt O06522 · UniProt O06523 · UniProt O06524
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