Research workbench
Monoclinic form of human IGA1 Fab fragment, sharing same fv as IgG
Analyse Monoclinic form of human IGA1 Fab fragment, sharing same fv as IgG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QNY
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment of immunoglobulin A1 light chain; Fab fragment of immunoglobulin A1 heavy…
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab fragment of immunoglobulin A1 light chain | protein | 218 | 7% helix, 50% strand | — |
| B | Fab fragment of immunoglobulin A1 heavy chain | protein | 213 | 6% helix, 50% strand | — |
| C | Fab fragment of immunoglobulin A1 light chain | protein | 219 | 7% helix, 50% strand | — |
| D | Fab fragment of immunoglobulin A1 heavy chain | protein | 210 | 6% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.63 | 0.76 | 69 | empty |
| 2 | 477 | 0.62 | 0.76 | 58 | empty |
| 3 | 338 | 0.57 | 0.76 | 27 | empty |
| 4 | 244 | 0.53 | 0.77 | 33 | empty |
| 5 | 134 | 0.49 | 0.79 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1669 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1542 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 566 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3QNY · Monoclinic form of human IgA1 Fab fragment, sharing same Fv as IgG · 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 3QNY · PDBe 3QNY
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