MolNFT v1 · #102175 · protein
Unliganded Fab structure of lipid a-specific antibody A6
4ODW · A6 Fab (IGG2B kappa) light chain: “Unliganded Fab structure of lipid a-specific antibody A6”. X-ray diffraction, 7 pockets (best druggability 0.58). MolNFT v1 #102175 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4ODW
- Type
- protein
- Length
- 850 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A6 Fab (IGG2B kappa) light chain; A6 Fab (IGG2B) heavy chain
- Pockets
- 7 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, B | A6 Fab (IGG2B kappa) light chain | protein | 214 | 7% helix, 50% strand | — |
| H | A6 Fab (IGG2B) heavy chain | protein | 214 | 6% helix, 56% strand | — |
| A | A6 Fab (IGG2B) heavy chain | protein | 208 | 7% helix, 58% strand | — |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.58 | 0.74 | 46 | TRS |
| 2 | 336 | 0.55 | 0.75 | 44 | empty |
| 3 | 108 | 0.39 | 0.75 | 25 | empty |
| 4 | 100 | 0.37 | 0.75 | 22 | empty |
| 5 | 65 | 0.35 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- B–A · 2126 Ų buried · 24 hydrogen bonds · protein-protein
- L–H · 2074 Ų buried · 19 hydrogen bonds · protein-protein
- H–A · 127 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4ODW · Unliganded Fab structure of lipid A-specific antibody A6 · 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 4ODW · PDBe 4ODW
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