MolNFT v1 · #151986 · protein
Fab fragment of an antibody selective for wild-type alpha-1- antitrypsin in complex with its antigen
6I3Z · Alpha-1-antitrypsin: “Fab fragment of an antibody selective for wild-type alpha-1- antitrypsin in complex with its antigen”. X-ray diffraction, 2 ligands (NA, SO4), 8 pockets (best druggability 0.74). MolNFT v1 #151986 on GenesisL1…
- PDB
- 6I3Z
- Type
- protein
- Length
- 759 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-1-antitrypsin; Fab 2H2 heavy chain; Fab 2H2 light chain
- UniProt
- P01009
- Ligands
- NA, SO4
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-1-antitrypsin | protein | 315 | 30% helix, 30% strand | P01009 |
| B | Alpha-1-antitrypsin | protein | 34 | 0% helix, 50% strand | P01009 |
| H | Fab 2H2 heavy chain | protein | 202 | 1% helix, 50% strand | — |
| L | Fab 2H2 light chain | protein | 208 | 6% helix, 50% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 235 | 0.74 | 0.88 | 44 | empty |
| 2 | 138 | 0.54 | 0.81 | 21 | empty |
| 3 | 284 | 0.52 | 0.74 | 44 | empty |
| 4 | 203 | 0.49 | 0.76 | 32 | empty |
| 5 | 94 | 0.46 | 0.80 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2253 Ų buried · 30 hydrogen bonds · protein-protein
- H–L · 1576 Ų buried · 8 hydrogen bonds · protein-protein
- A–H · 423 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 281 Ų buried · 4 hydrogen bonds · protein-protein
- B–H · 76 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6I3Z · Fab fragment of an antibody selective for wild-type alpha-1-antitrypsin in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P01009 · AlphaFold monomer V2.0 prediction for alpha-1-antitrypsin (P01009) · a predicted model of the same protein · chain A against A, TM-score 0.92
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P01009
- Elsewhere: RCSB PDB 6I3Z · PDBe 6I3Z · UniProt P01009
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