Research workbench

Fab fragment in complex with small molecule hapten, crystal form-1

Analyse Fab fragment in complex with small molecule hapten, crystal form-1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2JB5
Type: protein
Length: 427 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab fragment MOR03268 heavy chain; Fab fragment MOR03268 light chain
Ligands: T5C
Pockets: 6 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab fragment MOR03268 heavy chain	protein	216	8% helix, 52% strand	—
L	Fab fragment MOR03268 light chain	protein	211	5% helix, 46% strand	—

Ligands and binding sites

T5C · 2-{(1E,3Z,5E,7E)-7-[3,3-dimethyl-5-sulfo-1-(2-sulfoethyl)-1,3-dihydro-2H-indol-2-ylidene]-4-methylhepta-1,3,5-trien-1-yl}-3,3-dimethyl-5-sulfo-1-(2-sulfoethyl)-3H-indolium · ligand · chains H, L

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

Pockets

6 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	385	0.54	0.73	53	empty
2	163	0.50	0.77	20	T5C
3	61	0.42	0.82	13	empty
4	102	0.38	0.75	20	empty
5	86	0.36	0.75	19	empty

Interfaces

1 interface between chains.

H–L · 1688 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

2JB5 · Fab fragment in complex with small molecule hapten, crystal form-1 · 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 2JB5 · PDBe 2JB5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.