Research workbench
Crystal structure of S25-26 in complex with KDO(2.8)KDO(2.4)KDO trisaccharide
Analyse Crystal structure of S25-26 in complex with KDO(2.8)KDO(2.4)KDO trisaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M7J
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S25-26 Fab (IGG1K) heavy chain; S25-26 Fab (IGG1K) light chain
- Ligands
- KDA, KDO, NAG, K
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | S25-26 Fab (IGG1K) heavy chain | protein | 219 | 4% helix, 48% strand | — |
| L | S25-26 Fab (IGG1K) light chain | protein | 219 | 5% helix, 50% strand | — |
Ligands and binding sites
- KDA · prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid · ligand · chains H
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains H, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- K · Potassium ion · metal · chains H
- PEG · Di(hydroxyethyl)ether · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.53 | 0.80 | 27 | empty |
| 2 | 302 | 0.51 | 0.73 | 53 | empty |
| 3 | 120 | 0.44 | 0.77 | 23 | empty |
| 4 | 57 | 0.28 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- H–L · 2085 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4M7J · Crystal structure of S25-26 in complex with Kdo(2.8)Kdo(2.4)Kdo trisaccharide · the same entry in another collection · chain H against H, 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 4M7J · PDBe 4M7J
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