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Structure of the 1121B Fab fragment

Analyse Structure of the 1121B Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S34
Type: protein
Length: 427 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.2
Source: Mus musculus, Homo sapiens
Molecule: 1121B Fab light chain; 1121B Fab heavy chain
Ligands: PO4
Pockets: 4 · best druggability 0.64

Structure

x-ray diffraction · resolution 2.2 · 2 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	1121B Fab light chain	protein	214	6% helix, 51% strand	—
H	1121B Fab heavy chain	protein	213	8% helix, 53% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · chains H

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	571	0.64	0.75	58	empty
2	185	0.50	0.77	33	empty
3	92	0.42	0.78	22	empty
4	98	0.33	0.73	20	empty

Interfaces

1 interface between chains.

L–H · 1721 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

3S34 · Structure of the 1121B 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 3S34 · PDBe 3S34

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