Research workbench
S45-18 Fab pentasaccharide bisphosphate complex
Analyse S45-18 Fab pentasaccharide bisphosphate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Q9W
- Type
- protein
- Length
- 890 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S45-18 Fab (IGG1K) light chain; S45-18 Fab (IGG1K) heavy chain
- Ligands
- GP1, GP4, KDO, MG
- Pockets
- 13 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | S45-18 Fab (IGG1K) light chain | protein | 219 | 5% helix, 51% strand | — |
| B, D | S45-18 Fab (IGG1K) heavy chain | protein | 226 | 4% helix, 48% strand | — |
Ligands and binding sites
- GP1 · 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand · chains B
- GP4 · 2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose · ligand
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 6 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.64 | 0.74 | 72 | empty |
| 2 | 411 | 0.57 | 0.74 | 47 | empty |
| 3 | 62 | 0.57 | 0.90 | 17 | empty |
| 4 | 175 | 0.51 | 0.78 | 28 | empty |
| 5 | 188 | 0.50 | 0.77 | 28 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2016 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2015 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1Q9W · S45-18 Fab pentasaccharide bisphosphate complex · 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
- Elsewhere: RCSB PDB 1Q9W · PDBe 1Q9W
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