Research workbench
Crystal structure of processed tolb in complex with pal
Analyse Crystal structure of processed tolb in complex with pal in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W8B
- Type
- protein
- Length
- 2,063 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein tolb; Peptidoglycan-associated lipoprotein
- UniProt
- P0A855, P0A912
- Ligands
- SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein tolb | protein | 409 | 10% helix, 44% strand | P0A855 |
| B, D, F | Protein tolb | protein | 409 | 10% helix, 44% strand | P0A855 |
| C | Peptidoglycan-associated lipoprotein | protein | 104 | 39% helix, 17% strand | P0A912 |
| E | Peptidoglycan-associated lipoprotein | protein | 107 | 44% helix, 20% strand | P0A912 |
| G, H | Peptidoglycan-associated lipoprotein | protein | 108 | 44% helix, 17% strand | P0A912 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, H, B, D, F, G
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D, F
- ACT · Acetate ion · additive · 4 copies · chains A, B, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.82 | 0.90 | 39 | empty |
| 2 | 405 | 0.82 | 0.90 | 39 | empty |
| 3 | 417 | 0.81 | 0.89 | 39 | empty |
| 4 | 418 | 0.81 | 0.89 | 40 | empty |
| 5 | 915 | 0.74 | 0.78 | 99 | empty |
Interfaces
10 interfaces between chains.
- A–H · 1227 Ų buried · 16 hydrogen bonds · protein-protein
- F–G · 1227 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1216 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1203 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 722 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2W8B · Crystal structure of processed TolB in complex with Pal · 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 B against A, TM-score 1.00
- P0A912 · AlphaFold monomer V2.0 prediction for peptidoglycan-associated lipoprotein (P0A912) · a predicted model of the same protein · chain G against A, TM-score 0.97
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 P0A912
- Elsewhere: RCSB PDB 2W8B · PDBe 2W8B · UniProt P0A855 · UniProt P0A912
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