Research workbench
Crystal structure of S73-2 antibody in complex with antigen KDO(2.8) KDO(2.4)KDO
Analyse Crystal structure of S73-2 antibody in complex with antigen KDO(2.8) KDO(2.4)KDO in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HZV
- Type
- protein
- Length
- 438 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S73-2 Fab (IGG1K) light chain; S73-2 Fab (IGG1K) heavy chain
- Ligands
- KDA, KDO, MG, ZN
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S73-2 Fab (IGG1K) light chain | protein | 218 | 5% helix, 53% strand | — |
| B | S73-2 Fab (IGG1K) heavy chain | protein | 220 | 8% helix, 50% strand | — |
Ligands and binding sites
- KDA · prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid · ligand · chains B
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 588 | 0.63 | 0.75 | 62 | empty |
| 2 | 102 | 0.38 | 0.75 | 23 | empty |
| 3 | 73 | 0.30 | 0.74 | 20 | empty |
| 4 | 55 | 0.25 | 0.72 | 13 | KDO |
Interfaces
1 interface between chains.
- A–B · 1791 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3HZV · Crystal structure of S73-2 antibody in complex with antigen Kdo(2.8)Kdo(2.4)Kdo · 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 3HZV · PDBe 3HZV
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