5B6F | pdb_00005b6f

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.222 (Depositor), 0.222 (DCC)
R-Value Work:
0.195 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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

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| 3D Structure

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	3D Interactions
LTX Query on LTX Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain T [auth G] SDF format, chain P [auth E] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain T [auth G] MOL2 format, chain P [auth E] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain T [auth G] mmCIF format, chain P [auth E]	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		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain P [auth E] Focus chain T [auth G] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain P [auth E] Focus chain T [auth G]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain V [auth H] SDF format, chain R [auth F] SDF format, chain O [auth D] SDF format, chain K [auth B] MOL2 format, chain V [auth H] MOL2 format, chain R [auth F] MOL2 format, chain O [auth D] MOL2 format, chain K [auth B] mmCIF format, chain V [auth H] mmCIF format, chain R [auth F] mmCIF format, chain O [auth D] mmCIF format, chain K [auth B]	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		Interactions Focus chain K [auth B] Focus chain O [auth D] Focus chain R [auth F] Focus chain V [auth H] Interactions & Density Focus chain K [auth B] Focus chain O [auth D] Focus chain R [auth F] Focus chain V [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain U [auth H] SDF format, chain S [auth G] SDF format, chain Q [auth E] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] MOL2 format, chain U [auth H] MOL2 format, chain S [auth G] MOL2 format, chain Q [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] mmCIF format, chain U [auth H] mmCIF format, chain S [auth G] mmCIF format, chain Q [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B]	J [auth B] M [auth C] N [auth D] Q [auth E] S [auth G] 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		Interactions Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [auth G] Focus chain U [auth H] Interactions & Density Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [auth G] Focus chain U [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.222 (Depositor), 0.222 (DCC)
R-Value Work: 0.195 (Depositor), 0.196 (DCC)
R-Value Observed: 0.197 (Depositor)

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

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-05-31

Deposition Author(s):

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

Revision History (Full details and data files)

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