5KVL | pdb_00005kvl

Humanized 10G4 anti-leukotriene C4 antibody Fab fragment in complex with leukotriene C4

PDB DOI: https://doi.org/10.2210/pdb5KVL/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2016-07-14 Released: 2017-05-24
Deposition Author(s): Huxford, T., King, A., Fleming, J.K., Wojciak, J.M.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Humanized 10G4 anti-leukotriene C4 antibody Fab fragment in complex with leukotriene C4

Huxford, T., King, A., Fleming, J.K., Wojciak, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 47.44 kDa
Atom Count: 3,695
Modeled Residue Count: 429
Deposited Residue Count: 429
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Humanized 10G4 anti-Leukotriene C4 Immunoglobulin G (IgG) heavy chain Fab fragment	A [auth H]	215	Homo sapiens	Mutation(s): 0 Gene Names: IGHG1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Humanized 10G4 anti-Leukotriene C4 Immunoglobulin G (IgG) light chain	B [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LTX Query on LTX Download Ideal Coordinates CCD File SDF format, chain G [auth H] MOL2 format, chain G [auth H] mmCIF format, chain G [auth H]	G [auth H]	(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 G [auth H] Interactions & Density Focus chain G [auth H]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain E [auth H] MOL2 format, chain E [auth H] mmCIF format, chain E [auth H]	E [auth H]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain E [auth H] Interactions & Density Focus chain E [auth H]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain F [auth H] MOL2 format, chain F [auth H] mmCIF format, chain F [auth H]	F [auth H]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain F [auth H] Interactions & Density Focus chain F [auth H]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain I [auth L] SDF format, chain H [auth L] SDF format, chain C [auth H] MOL2 format, chain I [auth L] MOL2 format, chain H [auth L] MOL2 format, chain C [auth H] mmCIF format, chain I [auth L] mmCIF format, chain H [auth L] mmCIF format, chain C [auth H]	C [auth H], H [auth L], I [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth H] Focus chain H [auth L] Focus chain I [auth L] Interactions & Density Focus chain C [auth H] Focus chain H [auth L] Focus chain I [auth L]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth H] MOL2 format, chain D [auth H] mmCIF format, chain D [auth H]	D [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Interactions & Density Focus chain D [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.190 (Depositor), 0.190 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.88	α = 90
b = 41.631	β = 104.69
c = 93.126	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-05-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1112547

Revision History (Full details and data files)

Version 1.0: 2017-05-24
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Structure summary
Version 1.2: 2019-11-27
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.4: 2024-10-30
Changes: Structure summary