MolNFT v1 · #171721 · protein
Crystal structure of the Fab fragment of a glycosylated lymphoma antibody
6ZEC · Fab fragment light chain: “Crystal structure of the Fab fragment of a glycosylated lymphoma antibody”. X-ray diffraction, 2 ligands (NAG, MG), 2 pockets (best druggability 0.60). MolNFT v1 #171721 on GenesisL1: 3D structure, binding…
- PDB
- 6ZEC
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment light chain; Fab fragment heavy chain
- Ligands
- NAG, MG
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab fragment light chain | protein | 219 | 5% helix, 52% strand | — |
| H | Fab fragment heavy chain | protein | 222 | 11% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains L, H
- MG · Magnesium ion · metal · 2 copies · chains H
- GOL · Glycerol · additive · 2 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.60 | 0.75 | 52 | GOL |
| 2 | 149 | 0.45 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- L–H · 1909 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6ZEC · Crystal Structure of the Fab Fragment of a Glycosylated Lymphoma Antibody · 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 6ZEC · PDBe 6ZEC
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