Research workbench
Structure of the rhs-repeat containing bc component of the secreted ABC toxin complex from yersinia entomophaga
Analyse Structure of the rhs-repeat containing bc component of the secreted ABC toxin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IGL
- Type
- protein
- Length
- 4,240 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Yenb; YENC2
- UniProt
- B6A880, B6A882
- Ligands
- K
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Yenb | protein | 1457 | 11% helix, 39% strand | B6A880 |
| B | YENC2 | protein | 666 | 5% helix, 46% strand | B6A882 |
| C | Yenb | protein | 1449 | 11% helix, 39% strand | B6A880 |
| D | YENC2 | protein | 668 | 5% helix, 47% strand | B6A882 |
Ligands and binding sites
- K · Potassium ion · metal · 6 copies · chains A, B, C, D
- GOL · Glycerol · additive · 8 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.81 | 0.82 | 105 | empty |
| 2 | 856 | 0.80 | 0.83 | 104 | GOL |
| 3 | 338 | 0.76 | 0.87 | 47 | GOL |
| 4 | 1172 | 0.76 | 0.78 | 111 | empty |
| 5 | 349 | 0.75 | 0.86 | 45 | empty |
Interfaces
3 interfaces between chains.
- C–D · 3985 Ų buried · 60 hydrogen bonds · protein-protein
- A–B · 3950 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 1498 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4IGL · Structure of the RHS-repeat containing BC component of the secreted ABC toxin complex… · the same entry in another collection · chain D against D, TM-score 1.00
- B6A882 · AlphaFold monomer V2.0 prediction for toxin subunit YENC2 (B6A882) · a predicted model of the same protein · chain B against A, TM-score 0.99
- B6A880 · AlphaFold monomer V2.0 prediction for toxin subunit yenb (B6A880) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 B6A880
- Every structure of UniProt B6A882
- Elsewhere: RCSB PDB 4IGL · PDBe 4IGL · UniProt B6A880 · UniProt B6A882
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