Research workbench
S25-5 Fab in complex with chlamydiaceae-specific lps antigen
Analyse S25-5 Fab in complex with chlamydiaceae-specific lps antigen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C5H
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab heavy chain (IGG1); Fab light chain (IGG1 kappa)
- UniProt
- Q99LC4, A0A0F7R5U8
- Ligands
- GP1, Z9M, TAM, KDO, NAG, FUC, CL
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab heavy chain (IGG1) | protein | 213 | 7% helix, 51% strand | Q99LC4 |
| L | Fab light chain (IGG1 kappa) | protein | 216 | 6% helix, 54% strand | A0A0F7R5U8 |
Ligands and binding sites
- GP1 · 2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose · ligand
- Z9M · 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose · ligand · chains H
- TAM · Tris(hydroxyethyl)aminomethane · ligand · chains H
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 3 copies · chains H, L
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- FUC · alpha-L-fucopyranose · sugar · chains H
- CL · Chloride ion · ion · chains L
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains H
- PG4 · Tetraethylene glycol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.47 | 0.74 | 33 | PEG |
| 2 | 95 | 0.40 | 0.77 | 21 | empty |
| 3 | 139 | 0.36 | 0.72 | 21 | empty |
Interfaces
1 interface between chains.
- H–L · 1954 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 6C5H · S25-5 Fab in complex with Chlamydiaceae-specific LPS antigen · 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
- Every structure of UniProt Q99LC4
- Every structure of UniProt A0A0F7R5U8
- Elsewhere: RCSB PDB 6C5H · PDBe 6C5H · UniProt Q99LC4 · UniProt A0A0F7R5U8
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