5B6F

Crystal structure of the Fab fragment of an anti-Leukotriene C4 monoclonal antibody complexed with LTC4

• PDB DOI: https://doi.org/10.2210/pdb5B6F/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2016-05-27 Released: 2017-05-31 
• Deposition Author(s): Sugahara, M., Ago, H., Saino, H., Miyano, M.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology, RIKEN

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.222 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Literature

Crystal structure of the Fab fragment of an anti-Leukotriene C4 monoclonal antibody complexed with LTC4

Sugahara, M., Ago, H., Saino, H., Miyano, M., Yamamoto, S., Takahashi, Y.

To be published.

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)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 212.52 kDa 
• Atom Count: 14,756 
• Modelled Residue Count: 1,710 
• Deposited Residue Count: 1,900 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-leukotriene C4 monoclonal antibody immunoglobulin kappa light chain	A, C, E, G	238	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti-leukotriene C4 monoclonal antibody immunoglobulin gamma1 heavy chain	B, D, F, H	237	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LTX	I [auth A], L [auth C], P [auth E], T [auth G]	(5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2-[[(4~{S})-4-azanyl-5-oxidanyl-5-oxidanylidene-pentanoyl]amino]-3-( 2-hydroxy-2-oxoethylamino)-3-oxidanylidene-propyl]sulfanyl-5-oxidanyl-icosa-7,9,11,14-tetraenoic acid C30 H47 N3 O9 S GWNVDXQDILPJIG-NXOLIXFESA-N
MES	K [auth B], O [auth D], R [auth F], V [auth H]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	J [auth B], M [auth C], N [auth D], Q [auth E], S [auth G], U [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.222 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.6	α = 90
b = 173.98	β = 90.63
c = 75.46	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
REFMAC	refinement
iMOSFLM	data processing
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Sugahara, M., Ago, H., Saino, H., Miyano, M.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology	Japan	S1311005
RIKEN	Japan	--

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 2.0: 2019-07-24
  Changes: Advisory, Data collection, Database references, Experimental preparation, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary