Research workbench
Crystal structure of Fab WN1 222-5 in complex with lps
Analyse Crystal structure of Fab WN1 222-5 in complex with lps in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V0W
- Type
- protein
- Length
- 425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- WN1 222-5 Fab (IGG2A) light chain; WN1 222-5 Fab (IGG2A) heavy chain
- Ligands
- GM0, PA1, GLC, KDO, GLA, GMH, SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | WN1 222-5 Fab (IGG2A) light chain | protein | 211 | 6% helix, 53% strand | — |
| H | WN1 222-5 Fab (IGG2A) heavy chain | protein | 214 | 7% helix, 51% strand | — |
Ligands and binding sites
- GM0 · 4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose · ligand · 2 copies · chains H, L
- PA1 · 2-amino-2-deoxy-alpha-D-glucopyranose · ligand
- GLC · alpha-D-glucopyranose · sugar · 3 copies · chains H
- KDO · 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid · sugar · 2 copies · chains H
- GLA · alpha-D-galactopyranose · sugar · chains H
- GMH · L-glycero-alpha-D-manno-heptopyranose · sugar · chains H
- SO4 · Sulfate ion · ion · 10 copies · chains L, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.63 | 0.74 | 55 | empty |
| 2 | 117 | 0.40 | 0.75 | 25 | empty |
| 3 | 63 | 0.29 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- L–H · 1843 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3V0W · Crystal structure of Fab WN1 222-5 in complex with LPS · the same entry in another collection · chain L against L, 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 3V0W · PDBe 3V0W
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