MolNFT v1 · #41034 · protein

Fab fragment in complex with small molecule hapten, crystal form-2

2JB6 · Fab fragment MOR03268 light chain: “Fab fragment in complex with small molecule hapten, crystal form-2”. X-ray diffraction, 1 ligand (T5C), 11 pockets (best druggability 0.56). MolNFT v1 #41034 on GenesisL1: 3D structure, binding…

PDB: 2JB6
Type: protein
Length: 846 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab fragment MOR03268 light chain; Fab fragment MOR03268 heavy chain
Ligands: T5C
Pockets: 11 · best druggability 0.56

Structure

x-ray diffraction · 4 distinct chains · 6% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab fragment MOR03268 light chain	protein	211	7% helix, 48% strand	—
B	Fab fragment MOR03268 heavy chain	protein	213	6% helix, 53% strand	—
H	Fab fragment MOR03268 heavy chain	protein	212	3% helix, 53% strand	—
L	Fab fragment MOR03268 light chain	protein	210	8% helix, 48% 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 · 2 copies · chains A, B, H, L

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

Pockets

11 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	416	0.56	0.73	51	empty
2	425	0.56	0.73	59	empty
3	157	0.52	0.79	22	T5C
4	159	0.50	0.77	23	T5C
5	121	0.47	0.79	25	empty

Interfaces

3 interfaces between chains.

H–L · 1675 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1675 Å² buried · 18 hydrogen bonds · protein-protein
A–L · 593 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2JB6 · Fab fragment in complex with small molecule hapten, crystal form-2 · the same entry in another collection · chain A against A, 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 2JB6 · PDBe 2JB6

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