6QB9 | pdb_00006qb9

Structure of an anti-Mcl1 scFv

• PDB DOI: https://doi.org/10.2210/pdb6QB9/pdb

• Classification: APOPTOSIS
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2018-12-20 Released: 2019-11-06 
• Deposition Author(s): Hargreaves, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Antibody fragments structurally enable a drug-discovery campaign on the cancer target Mcl-1.

Luptak, J., Bista, M., Fisher, D., Flavell, L., Gao, N., Wickson, K., Kazmirski, S.L., Howard, T., Rawlins, P.B., Hargreaves, D.

(2019) Acta Crystallogr D Struct Biol 75: 1003-1014

• PubMed: 31692474 
• DOI: https://doi.org/10.1107/S2059798319014116
• Primary Citation Related Structures: 
  6QB3, 6QB4, 6QB6, 6QB9, 6QBC, 6QF9, 6QFC


• PubMed Abstract: 
  

  Apoptosis is a crucial process by which multicellular organisms control tissue growth, removal and inflammation. Disruption of the normal apoptotic function is often observed in cancer, where cell death is avoided by the overexpression of anti-apoptotic proteins of the Bcl-2 (B-cell lymphoma 2) family, including Mcl-1 (myeloid cell leukaemia 1). This makes Mcl-1 a potential target for drug therapy, through which normal apoptosis may be restored by inhibiting the protective function of Mcl-1. Here, the discovery and biophysical properties of an anti-Mcl-1 antibody fragment are described and the utility of both the scFv and Fab are demonstrated in generating an Mcl-1 crystal system amenable to iterative structure-guided drug design.

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Organizational Affiliation: 
• Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge CB4 0WG, England.
Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Waltham, MA 02451, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 53.16 kDa 
• Atom Count: 3,758 
• Modeled Residue Count: 473 
• Deposited Residue Count: 510 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv55	A, B [auth X]	255	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TLA (Subject of Investigation/LOI)	C [auth X], D [auth X]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.88	α = 90
b = 63.03	β = 109.96
c = 101.7	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-11-06 
Deposition Author(s): Hargreaves, D.

Revision History  

• Version 1.0: 2019-11-06
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary