2WEK | pdb_00002wek

Crystal structure of the human MGC45594 gene product in complex with diclofenac

PDB DOI: https://doi.org/10.2210/pdb2WEK/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-03-31 Released: 2009-12-15
Deposition Author(s): Shafqat, N., Yue, W.W., Ugochukwu, E., Niesen, F., Smee, C., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.214 (Depositor), 0.232 (DCC)
R-Value Work:
0.165 (Depositor), 0.189 (DCC)
R-Value Observed:
0.168 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Human Mgc45594 Gene Product in Complex with Diclofenac

Shafqat, N., Yue, W.W., Niesen, F., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 77.11 kDa
Atom Count: 5,679
Modeled Residue Count: 681
Deposited Residue Count: 682
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ZINC-BINDING ALCOHOL DEHYDROGENASE DOMAIN-CONTAINING PROTEIN 2	A, B	341	Homo sapiens	Mutation(s): 0 EC: 1 (PDB Primary Data), 1.3.1.48 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N4Q0 (Homo sapiens) Explore Q8N4Q0 Go to UniProtKB: Q8N4Q0
PHAROS: Q8N4Q0 GTEx: ENSG00000180011
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8N4Q0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain N [auth B] MOL2 format, chain C [auth A] MOL2 format, chain N [auth B] mmCIF format, chain C [auth A] mmCIF format, chain N [auth B]	C [auth A], N [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain N [auth B]
DIF Query on DIF Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] O [auth B] D [auth A], E [auth A], F [auth A], G [auth A], O [auth B], P [auth B], Q [auth B], R [auth B]	2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID C₁₄ H₁₁ Cl₂ N O₂ DCOPUUMXTXDBNB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain H [auth A] MOL2 format, chain S [auth B] MOL2 format, chain H [auth A] mmCIF format, chain S [auth B] mmCIF format, chain H [auth A]	H [auth A], S [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain S [auth B] Interactions & Density Focus chain H [auth A] Focus chain S [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth A] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth A] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth A] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain K [auth A]	J [auth A], K [auth A], L [auth A], T [auth B], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain T [auth B] Focus chain U [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth A] SDF format, chain V [auth B] MOL2 format, chain I [auth A] MOL2 format, chain M [auth A] MOL2 format, chain V [auth B] mmCIF format, chain I [auth A] mmCIF format, chain M [auth A] mmCIF format, chain V [auth B]	I [auth A], M [auth A], V [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain M [auth A] Focus chain V [auth B] Interactions & Density Focus chain I [auth A] Focus chain M [auth A] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.214 (Depositor), 0.232 (DCC)
R-Value Work: 0.165 (Depositor), 0.189 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.834	α = 94.61
b = 51.572	β = 91.54
c = 75.716	γ = 101.72

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-12-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.3: 2025-10-01
Changes: Derived calculations, Structure summary