Research workbench
The crystal structure of the tolb box of colicin a in complex with tolb reveals important differences in the recruitment of the common tolb translocation portal used by group a colicins
Analyse The crystal structure of the tolb box of colicin a in complex with tolb reveals… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IAX
- Type
- protein
- Length
- 411 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein tolb; Colicin-a
- UniProt
- P0A855, P04480
- Ligands
- NA, CA
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein tolb | protein | 399 | 10% helix, 45% strand | P0A855 |
| B | Colicin-a | protein | 12 | 0% helix, 0% strand | P04480 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.81 | 0.89 | 39 | CA |
| 2 | 96 | 0.46 | 0.80 | 18 | empty |
| 3 | 62 | 0.38 | 0.79 | 16 | empty |
| 4 | 70 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 605 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3IAX · The crystal structure of the TolB box of Colicin A in complex with TolB reveals important… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A855 · AlphaFold monomer V2.0 prediction for tol-pal system protein tolb (P0A855) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P04480 · AlphaFold monomer V2.0 prediction for colicin-a (P04480) · a predicted model of the same protein · chain B against A, TM-score 0.35
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 P0A855
- Every structure of UniProt P04480
- Elsewhere: RCSB PDB 3IAX · PDBe 3IAX · UniProt P0A855 · UniProt P04480
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