Research workbench
PFA2 Fab fragment, monoclinic apo form
Analyse PFA2 Fab fragment, monoclinic apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IQA
- Type
- protein
- Length
- 879 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A Fab fragment PFA2 kappa light chain; IGG2A Fab fragment PFA2 heavy chain
- UniProt
- A2NHM3, Q811U5
- Ligands
- ACM, CL
- Pockets
- 12 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, A | IGG2A Fab fragment PFA2 kappa light chain | protein | 219 | 5% helix, 52% strand | A2NHM3 |
| H | IGG2A Fab fragment PFA2 heavy chain | protein | 221 | 5% helix, 49% strand | Q811U5 |
| B | IGG2A Fab fragment PFA2 heavy chain | protein | 220 | 4% helix, 49% strand | Q811U5 |
Ligands and binding sites
- ACM · Acetamide · ligand · 2 copies · chains L, H, A, B
- CL · Chloride ion · ion · chains H
- GOL · Glycerol · additive · 8 copies · chains L, H, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 559 | 0.71 | 0.80 | 49 | GOL |
| 2 | 440 | 0.57 | 0.74 | 54 | empty |
| 3 | 286 | 0.51 | 0.74 | 41 | empty |
| 4 | 76 | 0.44 | 0.80 | 16 | empty |
| 5 | 92 | 0.39 | 0.77 | 20 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1936 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1852 Ų buried · 23 hydrogen bonds · protein-protein
- H–B · 298 Ų buried · 6 hydrogen bonds · protein-protein
- L–B · 132 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 2IQA · PFA2 FAB fragment, monoclinic apo form · 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
- Every structure of UniProt A2NHM3
- Every structure of UniProt Q811U5
- Elsewhere: RCSB PDB 2IQA · PDBe 2IQA · UniProt A2NHM3 · UniProt Q811U5
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