MolNFT v1 · #170000 · protein
Ab 1116NS19.9 bound to CA19-9
6XTG · Light chain: “Ab 1116NS19.9 bound to CA19-9”. X-ray diffraction, 5 ligands (NAG, GAL, SIA), 6 pockets (best druggability 0.61). MolNFT v1 #170000 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XTG
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain; Heavy chain
- Ligands
- NAG, GAL, SIA, FUC, NA
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Light chain | protein | 214 | 6% helix, 51% strand | — |
| H | Heavy chain | protein | 216 | 9% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- GAL · beta-D-galactopyranose · sugar · chains L, H
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains L, H
- FUC · alpha-L-fucopyranose · sugar · chains L, H
- NA · Sodium ion · metal · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.61 | 0.74 | 58 | empty |
| 2 | 302 | 0.58 | 0.77 | 39 | empty |
| 3 | 52 | 0.45 | 0.85 | 21 | empty |
| 4 | 108 | 0.36 | 0.74 | 24 | empty |
| 5 | 72 | 0.33 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- L–H · 1676 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6XTG · Ab 1116NS19.9 bound to CA19-9 · 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 6XTG · PDBe 6XTG
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