MolNFT v1 · #161956 · protein
Fab fragment of an antibody that inhibits polymerisation of alpha-1- antitrypsin
6QU9 · Fab 4B12 heavy chain: “Fab fragment of an antibody that inhibits polymerisation of alpha-1- antitrypsin”. X-ray diffraction, 2 ligands (NA, SO4), 5 pockets (best druggability 0.77). MolNFT v1 #161956 on GenesisL1: 3D structure…
- PDB
- 6QU9
- Type
- protein
- Length
- 848 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 4B12 heavy chain; Fab 4B12 light chain
- Ligands
- NA, SO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab 4B12 heavy chain | protein | 215 | 7% helix, 50% strand | — |
| L | Fab 4B12 light chain | protein | 212 | 6% helix, 53% strand | — |
| A | Fab 4B12 heavy chain | protein | 210 | 6% helix, 52% strand | — |
| B | Fab 4B12 light chain | protein | 211 | 7% helix, 54% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains L
- SO4 · Sulfate ion · ion · 2 copies · chains H, A
- GOL · Glycerol · additive · 2 copies · chains L, A
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 | 1007 | 0.77 | 0.79 | 110 | GOL |
| 2 | 482 | 0.58 | 0.74 | 53 | GOL |
| 3 | 53 | 0.47 | 0.86 | 22 | empty |
| 4 | 118 | 0.40 | 0.75 | 19 | empty |
| 5 | 67 | 0.31 | 0.75 | 17 | empty |
Interfaces
4 interfaces between chains.
- H–L · 1821 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1609 Ų buried · 11 hydrogen bonds · protein-protein
- L–A · 328 Ų buried · 2 hydrogen bonds · protein-protein
- H–A · 131 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6QU9 · Fab fragment of an antibody that inhibits polymerisation of alpha-1-antitrypsin · 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 6QU9 · PDBe 6QU9
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