Research workbench
Single-particle cryo-EM structure of the waal O-antigen ligase in its apo state
Analyse Single-particle cryo-EM structure of the waal O-antigen ligase in its apo state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TPJ
- Type
- protein
- Length
- 626 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative cell surface polysaccharide POLYMERASE/LIGASE; Fab heavy (H) chain; Fab light…
- UniProt
- Q1LJU1
- Pockets
- 7 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Putative cell surface polysaccharide POLYMERASE/LIGASE | protein | 403 | 68% helix, 0% strand | Q1LJU1 |
| H | Fab heavy (H) chain | protein | 119 | 3% helix, 50% strand | — |
| L | Fab light (L) chain | protein | 104 | 3% helix, 40% strand | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.85 | 0.86 | 125 | empty |
| 2 | 67 | 0.56 | 0.88 | 21 | empty |
| 3 | 64 | 0.36 | 0.78 | 12 | empty |
| 4 | 58 | 0.33 | 0.77 | 19 | empty |
| 5 | 79 | 0.31 | 0.73 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–L · 950 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 868 Ų buried · 4 hydrogen bonds · protein-protein
- B–L · 452 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7TPJ · Single-Particle Cryo-EM Structure of the WaaL O-antigen ligase in its apo state · the same entry in another collection · chain B against B, 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 Q1LJU1
- Elsewhere: RCSB PDB 7TPJ · PDBe 7TPJ · UniProt Q1LJU1
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