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PFA2 Fab fragment, triclinic apo form

Analyse PFA2 Fab fragment, triclinic apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2IQ9
Type: protein
Length: 440 residues
Chains: 2
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
Ligands: ACM
Pockets: 6 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	IGG2A Fab fragment PFA2 kappa light chain	protein	219	7% helix, 51% strand	—
H	IGG2A Fab fragment PFA2 heavy chain	protein	221	4% helix, 50% strand	—

Ligands and binding sites

ACM · Acetamide · ligand · 2 copies · chains L, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	87	0.51	0.83	18	empty
2	249	0.49	0.74	37	empty
3	118	0.39	0.74	22	empty
4	81	0.34	0.74	18	empty
5	84	0.32	0.73	16	empty

Interfaces

1 interface between chains.

L–H · 1920 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 covalent (disulfide, covalent ligand).

Compared structures

2IQ9 · PFA2 FAB fragment, triclinic 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
Elsewhere: RCSB PDB 2IQ9 · PDBe 2IQ9

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