Research workbench
Protective antigen pore translocating lethal factor N-terminal domain
Analyse Protective antigen pore translocating lethal factor N-terminal domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KXR
- Type
- protein
- Length
- 4,154 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lethal factor; Protective antigen
- EC
- 3.4.24.83
- UniProt
- P15917, P13423
- Ligands
- CA
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 19% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Lethal factor (EC 3.4.24.83) | protein | 220 | 32% helix, 0% strand | P15917 |
| A, B, C, D, E, F, G | Protective antigen | protein | 562 | 15% helix, 41% strand | P13423 |
Ligands and binding sites
- CA · Calcium ion · metal · 14 copies · chains A, B, C, D, E, F, G
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 | 1019 | 0.88 | 0.89 | 136 | empty |
| 2 | 748 | 0.83 | 0.87 | 100 | empty |
| 3 | 662 | 0.81 | 0.86 | 91 | empty |
| 4 | 766 | 0.80 | 0.84 | 93 | empty |
| 5 | 1141 | 0.78 | 0.80 | 126 | empty |
Interfaces
14 interfaces between chains.
- B–C · 3740 Ų buried · 81 hydrogen bonds · protein-protein
- E–F · 3732 Ų buried · 75 hydrogen bonds · protein-protein
- D–E · 3711 Ų buried · 78 hydrogen bonds · protein-protein
- C–D · 3710 Ų buried · 78 hydrogen bonds · protein-protein
- A–B · 3708 Ų buried · 72 hydrogen bonds · protein-protein
Compared structures
- 7KXR · Protective antigen pore translocating lethal factor N-terminal domain · the same entry in another collection · chain G against G, TM-score 1.00
- P13423 · AlphaFold monomer V2.0 prediction for protective antigen (P13423) · a predicted model of the same protein · chain A against A, TM-score 0.79
- P15917 · AlphaFold monomer V2.0 prediction for lethal factor (P15917) · a predicted model of the same protein · chain L against A, TM-score 0.32
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 P15917
- Every structure of UniProt P13423
- Elsewhere: RCSB PDB 7KXR · PDBe 7KXR · UniProt P15917 · UniProt P13423
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