Research workbench
Crystal structure of S25-2 in complex with a 5,6-dehydro-kdo disaccharide
Analyse Crystal structure of S25-2 in complex with a 5,6-dehydro-kdo disaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HGW
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody Fab fragment, light chain; Antibody Fab fragment, heavy chain
- Ligands
- KTU, KDO, ZN
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody Fab fragment, light chain | protein | 217 | 6% helix, 52% strand | — |
| B | Antibody Fab fragment, heavy chain | protein | 213 | 7% helix, 51% strand | — |
Ligands and binding sites
- KTU · prop-2-en-1-yl 3,5-dideoxy-alpha-D-threo-oct-5-en-2-ulopyranosidonic acid · ligand · chains A, B
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.64 | 0.75 | 61 | empty |
| 2 | 70 | 0.29 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1765 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4HGW · Crystal structure of S25-2 in complex with a 5,6-dehydro-Kdo disaccharide · the same entry in another collection · 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
- Elsewhere: RCSB PDB 4HGW · PDBe 4HGW
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