3HKK | pdb_00003hkk

Structure of human Leukotriene C4 synthase in complex with glutathione sulfonate

PDB DOI: https://doi.org/10.2210/pdb3HKK/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2009-05-24 Released: 2010-05-26
Deposition Author(s): Rinaldo-Matthis, A., Haeggstrom, J.Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.232 (Depositor), 0.231 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Pre-steady state kinetics of human Leukotriene C4 synthase

Rinaldo-Matthis, A., Wetterholm, A., Holm, J., Ohlsson, E., Tibbelin, G., Morgenstern, R., Haeggstrom, J.Z.

To be published.

Macromolecule Content

Total Structure Weight: 19.56 kDa
Atom Count: 1,284
Modeled Residue Count: 145
Deposited Residue Count: 156
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukotriene C4 synthase	A	156	Homo sapiens	Mutation(s): 0 EC: 4.4.1.20 (PDB Primary Data), 2.5.1 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q16873 (Homo sapiens) Explore Q16873 Go to UniProtKB: Q16873
PHAROS: Q16873
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16873
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTS Query on GTS Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	GLUTATHIONE SULFONIC ACID C₁₀ H₁₇ N₃ O₉ S QGWRMTHFAZVWAM-WDSKDSINSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain D [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A]
PAM Query on PAM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PALMITOLEIC ACID C₁₆ H₃₀ O₂ SECPZKHBENQXJG-FPLPWBNLSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.232 (Depositor), 0.231 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.718	α = 90
b = 170.718	β = 90
c = 170.718	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PXSOFT	data collection
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-05-26

Deposition Author(s):

Rinaldo-Matthis, A.

Haeggstrom, J.Z.

Revision History (Full details and data files)

Version 1.0: 2010-05-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

3HKK | pdb_00003hkk

Structure of human Leukotriene C4 synthase in complex with glutathione sulfonate

Literature

Pre-steady state kinetics of human Leukotriene C4 synthase

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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