6NEX | pdb_00006nex

Fab fragment of anti-cocaine antibody h2E2

• PDB DOI: https://doi.org/10.2210/pdb6NEX/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2018-12-18 Released: 2019-11-20 
• Deposition Author(s): Pokkuluri, P.R., Tan, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.254 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.214 (Depositor) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of free and liganded forms of the Fab fragment of a high-affinity anti-cocaine antibody, h2E2.

Tan, K., Zhou, M., Ahrendt, A.J., Duke, N.E.C., Tabaja, N., Ball, W.J., Kirley, T.L., Norman, A.B., Joachimiak, A., Schiffer, M., Wilton, R., Pokkuluri, P.R.

(2019) Acta Crystallogr F Struct Biol Commun 75: 697-706

• PubMed: 31702583 
• DOI: https://doi.org/10.1107/S2053230X19013608
• Primary Citation Related Structures: 
  6NEX, 6NFN


• PubMed Abstract: 
  

  A high-affinity anti-cocaine monoclonal antibody, designated h2E2, is entering phase 1 clinical trials for cocaine abuse therapy. To gain insight into the molecular details of its structure that are important for binding cocaine and cocaine metabolites, the Fab fragment was generated and crystallized with and without ligand. Structures of the unliganded Fab and the Fab fragment bound to benzoylecgonine were determined, and were compared with each other and with other crystallized anti-cocaine antibodies. The affinity of the h2E2 antibody for cocaine is 4 nM, while that of the cocaine metabolite benzoylecgonine is 20 nM. Both are higher than the reported affinity for cocaine of the two previously crystallized anti-cocaine antibodies. Consistent with cocaine fluorescent quenching binding studies for the h2E2 mAb, four aromatic residues in the CDR regions of the Fab (TyrL32, TyrL96, TrpL91 and TrpH33) were found to be involved in ligand binding. The aromatic side chains surround and trap the tropane moiety of the ligand in the complex structure, forming significant van der Waals interactions which may account for the higher affinity observed for the h2E2 antibody. A water molecule mediates hydrogen bonding between the antibody and the carbonyl group of the benzoyl ester. The affinity of binding to h2E2 of benzoylecgonine differs only by a factor of five compared with that of cocaine; therefore, it is suggested that h2E2 would bind cocaine in the same way as observed in the Fab-benzoylecgonine complex, with minor rearrangements of some hypervariable segments of the antibody.

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Organizational Affiliation: 
• Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA.
Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA.
Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA.
Department of Pharmacology and Systems Physiology, College of Medicine and Microbiology, University of Cincinnati, Cincinnati, OH 45267, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.64 kDa 
• Atom Count: 6,486 
• Modeled Residue Count: 851 
• Deposited Residue Count: 866 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anitgen binding fragment light chain	A [auth L]	215	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen binding fragment heavy chain	B [auth H]	218	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Anitgen binding fragment light chain	C [auth A]	215	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Ighg protein	D [auth B]	218	Mus musculus	Mutation(s): 0  Gene Names: Ighg, AU044919

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	J [auth H]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
FMT	G [auth L], H [auth L], I [auth L], L [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CL	E [auth L], F [auth L], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	A [auth L]	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS
PCA	A [auth L]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.254 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.214 (Depositor) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.787	α = 90
b = 128.435	β = 125.258
c = 91.196	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Pokkuluri, P.R., Tan, K.

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 2.0: 2020-01-22
  Changes: Polymer sequence, Structure summary
• Version 2.1: 2024-04-03
  Changes: Data collection, Database references, Refinement description