Research workbench
Cdia-ct toxin from burkholderia pseudomallei E479 in complex with cognate cdii immunity protein
Analyse Cdia-ct toxin from burkholderia pseudomallei E479 in complex with cognate cdii… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J4A
- Type
- protein
- Length
- 440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA nuclease cdia; Immunity protein cdii
- EC
- 3.1.-.-
- UniProt
- H9T8G6, H9T8G7
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | TRNA nuclease cdia (EC 3.1.-.-) | protein | 116 | 52% helix, 14% strand | H9T8G6 |
| B, D | Immunity protein cdii | protein | 104 | 63% helix, 13% strand | H9T8G7 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.67 | 0.80 | 42 | empty |
| 2 | 118 | 0.52 | 0.81 | 24 | empty |
| 3 | 128 | 0.52 | 0.81 | 26 | empty |
| 4 | 181 | 0.44 | 0.74 | 23 | empty |
| 5 | 54 | 0.29 | 0.75 | 11 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1040 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1024 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 267 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 147 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5J4A · CdiA-CT toxin from Burkholderia pseudomallei E479 in complex with cognate CdiI immunity… · the same entry in another collection · chain D against D, TM-score 1.00
- H9T8G7 · AlphaFold monomer V2.0 prediction for immunity protein cdii (H9T8G7) · a predicted model of the same protein · chain B against A, TM-score 0.99
- H9T8G6 · AlphaFold monomer V2.0 prediction for tRNA nuclease cdia (H9T8G6) · a predicted model of the same protein · chain A 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 H9T8G6
- Every structure of UniProt H9T8G7
- Elsewhere: RCSB PDB 5J4A · PDBe 5J4A · UniProt H9T8G6 · UniProt H9T8G7
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