Research workbench
Human monoclonal antibody with a LAIR1 insertion
Analyse Human monoclonal antibody with a LAIR1 insertion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NST
- Type
- protein
- Length
- 1,076 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of antibody MGD21; Heavy chain of antibody MGD21
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light chain of antibody MGD21 | protein | 210 | 5% helix, 53% strand | — |
| B | Heavy chain of antibody MGD21 | protein | 336 | 4% helix, 50% strand | — |
| C | Light chain of antibody MGD21 | protein | 208 | 3% helix, 50% strand | — |
| D | Heavy chain of antibody MGD21 | protein | 322 | 5% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.78 | 0.80 | 105 | GOL |
| 2 | 745 | 0.73 | 0.79 | 78 | empty |
| 3 | 687 | 0.71 | 0.78 | 75 | empty |
| 4 | 495 | 0.59 | 0.74 | 52 | GOL |
| 5 | 292 | 0.50 | 0.73 | 40 | GOL |
Interfaces
5 interfaces between chains.
- C–D · 2134 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2079 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 583 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 128 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 116 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5NST · Human monoclonal antibody with a LAIR1 insertion · the same entry in another collection · chain A against A, 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 5NST · PDBe 5NST
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