MolNFT v1 · #3245 · protein
IgG Fab (human IGG1, kappa) chimeric fragment (CBR96) complexed with lewis Y nonoate methyl ester
1CLY: “IgG Fab (human IGG1, kappa) chimeric fragment (CBR96) complexed with lewis Y nonoate methyl ester”. X-ray diffraction, 4 ligands (NON, FUC, NAG), 5 pockets (best druggability 0.59). MolNFT v1 #3245 on GenesisL1: 3D structure…
- PDB
- 1CLY
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IgG Fab (human IGG1, kappa)
- Ligands
- NON, FUC, NAG, GAL
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IgG Fab (human IGG1, kappa) | protein | 217 | 6% helix, 52% strand | — |
| H | IgG Fab (human IGG1, kappa) | protein | 219 | 8% helix, 53% strand | — |
Ligands and binding sites
- NON · Methyl nonanoate (ester) · ligand · chains H
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains L, H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- GAL · beta-D-galactopyranose · sugar · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.59 | 0.74 | 54 | empty |
| 2 | 54 | 0.58 | 0.91 | 20 | empty |
| 3 | 96 | 0.37 | 0.76 | 26 | empty |
| 4 | 99 | 0.36 | 0.74 | 18 | NAG, GAL, FUC |
| 5 | 70 | 0.32 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- L–H · 2006 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1CLY · IgG Fab (human IGG1, kappa) chimeric fragment (CBR96) complexed with lewis Y nonoate… · 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
- Elsewhere: RCSB PDB 1CLY · PDBe 1CLY
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