Research workbench

Fab fragment of anti-cocaine antibody H2E2 bound to benzoylecgonine

Analyse Fab fragment of anti-cocaine antibody H2E2 bound to benzoylecgonine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NFN
Type: protein
Length: 3,371 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab H2E2 light chain; Fab H2E2 heavy chain
Ligands: BCG
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 15 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab H2E2 light chain	protein	211	8% helix, 53% strand	—
H	Fab H2E2 heavy chain	protein	204	9% helix, 48% strand	—
A	Fab H2E2 light chain	protein	213	7% helix, 51% strand	—
B	Fab H2E2 heavy chain	protein	206	6% helix, 50% strand	—
C	Fab H2E2 light chain	protein	212	7% helix, 52% strand	—
D	Fab H2E2 heavy chain	protein	209	6% helix, 53% strand	—
E, I	Fab H2E2 light chain	protein	213	7% helix, 51% strand	—
F	Fab H2E2 heavy chain	protein	212	8% helix, 50% strand	—
J	Fab H2E2 heavy chain	protein	219	8% helix, 52% strand	—
O	Fab H2E2 light chain	protein	212	8% helix, 52% strand	—
P	Fab H2E2 heavy chain	protein	209	9% helix, 52% strand	—
Q	Fab H2E2 light chain	protein	210	5% helix, 45% strand	—
R	Fab H2E2 heavy chain	protein	201	6% helix, 49% strand	—
M	Fab H2E2 light chain	protein	213	7% helix, 53% strand	—
N	Fab H2E2 heavy chain	protein	214	7% helix, 50% strand	—

Ligands and binding sites

BCG · 3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1]octane-2-carboxylic acid · ligand · 8 copies · chains L, H, A, B, C, D, E, F, I, J, O, P, Q, R, M, N
ACT · Acetate ion · additive · 9 copies · chains L, H, A, B, C, D, E, F, I, J, O, P, Q, R, M, N
PEG · Di(hydroxyethyl)ether · additive · chains L, I
GOL · Glycerol · additive · chains L
FMT · Formic acid · additive · chains O

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	784	0.76	0.80	103	empty
2	883	0.67	0.74	78	empty
3	901	0.67	0.73	103	empty
4	819	0.66	0.74	78	empty
5	720	0.65	0.74	69	empty

Interfaces

21 interfaces between chains.

I–J · 1953 Å² buried · 14 hydrogen bonds · protein-protein
M–N · 1844 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 1802 Å² buried · 16 hydrogen bonds · protein-protein
O–P · 1755 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 1695 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 35 disulfide (disulfide).

Compared structures

6NFN · Fab fragment of anti-cocaine antibody h2E2 bound to benzoylecgonine · the same entry in another collection · chain L against L, 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 6NFN · PDBe 6NFN

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