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Bacterial oligosaccharyltransferase PglB in complex with an inhibitory peptide and a reactive lipid-linked oligosaccharide analog
Analyse Bacterial oligosaccharyltransferase PglB in complex with an inhibitory peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GXC
- Type
- protein
- Length
- 714 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.401
- Source
- Campylobacter lari (strain RM2100 / D67 / ATCC BAA-1060); Campylobacter lari…
- Molecule
- Undecaprenyl-diphosphooligosaccharide--protein glycotransferase…
- EC
- 2.4.99.19
- UniProt
- B9KDD4
- Ligands
- FFK, MN, NA
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · resolution 3.401 · 2 distinct chains · 58% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl-diphosphooligosaccharide--protein glycotransferase (EC 2.4.99.19) | protein | 706 | 59% helix, 10% strand | B9KDD4 |
| B | Gly-asp-gln-dab-ala-thr-ppn-gly | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- FFK · [(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] [oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2, 6,10,14-tetraenoxy]phosphoryl] hydrogen phosphate · ligand · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.72 | 0.79 | 65 | FFK |
| 2 | 66 | 0.55 | 0.88 | 18 | empty |
| 3 | 120 | 0.52 | 0.81 | 24 | empty |
| 4 | 162 | 0.50 | 0.78 | 24 | empty |
| 5 | 137 | 0.48 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 770 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 6GXC · Bacterial oligosaccharyltransferase pglb in complex with an inhibitory peptide and a… · the same entry in another collection · chain A against A, TM-score 1.00
- B9KDD4 · AlphaFold monomer V2.0 prediction for undecaprenyl- diphosphooligosaccharide--protein… · a predicted model of the same protein · chain A against A, TM-score 1.00
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 B9KDD4
- Elsewhere: RCSB PDB 6GXC · PDBe 6GXC · UniProt B9KDD4
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