Research workbench
Structure of tolb in complex with a peptide of the colicin E9 T-domain
Analyse Structure of tolb in complex with a peptide of the colicin E9 T-domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IVZ
- Type
- protein
- Length
- 1,625 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein tolb; Colicin-E9
- EC
- 3.1.-.-
- UniProt
- P0A855, P09883
- Ligands
- CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 11% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein tolb | protein | 392 | 12% helix, 44% strand | P0A855 |
| C | Protein tolb | protein | 391 | 12% helix, 43% strand | P0A855 |
| D | Protein tolb | protein | 387 | 12% helix, 44% strand | P0A855 |
| E | Colicin-E9 (EC 3.1.-.-) | protein | 15 | 0% helix, 0% strand | P09883 |
| F, G, H | Colicin-E9 (EC 3.1.-.-) | protein | 16 | 0% helix, 0% strand | P09883 |
Ligands and binding sites
- CA · Calcium ion · metal · 7 copies · chains A, B, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 408 | 0.81 | 0.90 | 39 | CA |
| 2 | 402 | 0.81 | 0.90 | 39 | CA |
| 3 | 405 | 0.81 | 0.90 | 39 | CA |
| 4 | 399 | 0.81 | 0.90 | 39 | CA |
| 5 | 66 | 0.47 | 0.83 | 19 | empty |
Interfaces
8 interfaces between chains.
- B–F · 734 Ų buried · 9 hydrogen bonds · protein-protein
- C–G · 714 Ų buried · 9 hydrogen bonds · protein-protein
- D–H · 713 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 712 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 348 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2IVZ · Structure of TolB in complex with a peptide of the colicin E9 T- domain · the same entry in another collection · chain H against H, 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 C against A, TM-score 0.97
- P09883 · AlphaFold monomer V2.0 prediction for colicin-E9 (P09883) · a predicted model of the same protein · chain E against A, TM-score 0.26
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 P09883
- Elsewhere: RCSB PDB 2IVZ · PDBe 2IVZ · UniProt P0A855 · UniProt P09883
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