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Crystal structure of human IgG abt-325 Fab fragment

Analyse Crystal structure of human IgG abt-325 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VXV
Type: protein
Length: 436 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Human IgG abt-325
Pockets: 5 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Human IgG abt-325	protein	222	8% helix, 50% strand	—
L	Human IgG abt-325	protein	214	6% helix, 53% strand	—

Ligands and binding sites

CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains H
GOL · Glycerol · additive · chains H, L

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	283	0.58	0.77	35	empty
2	380	0.57	0.75	51	empty
3	50	0.51	0.88	21	GOL
4	83	0.40	0.78	14	empty
5	104	0.36	0.74	20	empty

Interfaces

1 interface between chains.

H–L · 1916 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2VXV · Crystal structure of human IgG ABT-325 Fab Fragment · 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 2VXV · PDBe 2VXV

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