Research workbench
S25-2- A(2-4)KDO disaccharide complex
Analyse S25-2- A(2-4)KDO disaccharide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T77
- Type
- protein
- Length
- 443 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S25-2 Fab (IGG1K) light chain; S25-2 Fab (IGG1K) heavy chain
- Ligands
- KDA, KDO, MG, ZN
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S25-2 Fab (IGG1K) light chain | protein | 219 | 7% helix, 52% strand | — |
| B | S25-2 Fab (IGG1K) heavy chain | protein | 224 | 8% helix, 48% strand | — |
Ligands and binding sites
- KDA · prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid · ligand · chains A, B
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains A
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 | 523 | 0.59 | 0.74 | 57 | empty |
| 2 | 226 | 0.57 | 0.79 | 32 | empty |
| 3 | 81 | 0.31 | 0.73 | 17 | empty |
| 4 | 75 | 0.29 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1886 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3T77 · S25-2- A(2-4)KDO disaccharide complex · 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 3T77 · PDBe 3T77
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