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Crystal structure of a theophylline binding antibody Fab fragment

Analyse Crystal structure of a theophylline binding antibody Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BMF
Type: protein
Length: 432 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab fragment heavy chain; Fab fragment light chain
Ligands: 4TJ
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab fragment heavy chain	protein	216	9% helix, 53% strand	—
L	Fab fragment light chain	protein	216	6% helix, 51% strand	—

Ligands and binding sites

4TJ · 2-(5-{1-[1-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)-4,15-dioxo-8,11-dioxa-5,14-diazaicosan-20-yl]-3,3-dimethyl-6-sulfo-1,3-dihydro-2H-indol-2-ylidene}penta-1,3-dien-1-yl)-1-ethyl-3,3-dimethyl-3H-indolium-5-sulfonate · ligand · chains H, L

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

Pockets

3 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	493	0.59	0.74	57	empty
2	60	0.31	0.75	14	empty
3	70	0.27	0.72	17	empty

Interfaces

1 interface between chains.

H–L · 1769 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5BMF · Crystal Structure of a Theophylline binding antibody 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 5BMF · PDBe 5BMF

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