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Structure of bacterial oligosaccharyltransferase pglb in complex with an acceptor peptide and an lipid-linked oligosaccharide analog
Analyse Structure of bacterial oligosaccharyltransferase pglb in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OGL
- Type
- protein
- Length
- 715 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl-diphosphooligosaccharide--protein glycotransferase; Substrate mimicking…
- EC
- 2.4.99.19
- UniProt
- B9KDD4
- Ligands
- 9UB, MN, NA
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 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 | 707 | 58% helix, 11% strand | B9KDD4 |
| B | Substrate mimicking peptide | protein | 8 | 0% helix, 13% strand | — |
Ligands and binding sites
- 9UB · [(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]methyl-[oxidanyl-[(2~{Z},6~{Z},10~{Z})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraenoxy]phosphoryl]oxy-phosphinic acid · ligand · chains A
- MN · Manganese (II) ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.72 | 0.79 | 66 | MN, 9UB |
| 2 | 82 | 0.58 | 0.87 | 20 | empty |
| 3 | 117 | 0.52 | 0.82 | 24 | empty |
| 4 | 171 | 0.50 | 0.78 | 29 | empty |
| 5 | 128 | 0.48 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 789 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nonstandard).
Compared structures
- 5OGL · Structure of bacterial oligosaccharyltransferase PglB in complex with an acceptor peptide… · 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 5OGL · PDBe 5OGL · UniProt B9KDD4
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