1CQE

PROSTAGLANDIN H2 SYNTHASE-1 COMPLEX WITH FLURBIPROFEN

> Summary

Summary for 1CQE

DescriptorPROSTAGLANDIN H2 SYNTHASE-1 (E.C.1.14.99.1)
Functional Keywordsoxidoreductase, dioxygenase, peroxidase
Biological sourceOvis aries (sheep)
Cellular locationEndoplasmic reticulum membrane; Multi-pass membrane protein P05979
Total number of polymer chains8
Total molecular weight138921.76
Authors
Picot, D.,Loll, P.J.,Mulichak, A.M.,Garavito, R.M. (deposition date: 1999-06-15, release date: 1999-06-30, modification date: 2011-07-13)
Primary citation
Picot, D.,Loll, P.J.,Garavito, R.M.
The X-ray crystal structure of the membrane protein prostaglandin H2 synthase-1.
Nature, 367:243-249, 1994
PubMed: 8121489
DOI: 10.1038/367243a0
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.1 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliers110.2%5.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1cqe
no rotation
Molmil generated image of 1cqe
rotated about x axis by 90°
Molmil generated image of 1cqe
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, BPROTEIN (PROSTAGLANDIN H2 SYNTHASE-1)polymer58066596.02
UniProt (P05979)
Pfam (PF00008)
Pfam (PF03098)
Ovis aries (sheep)@PDBjCYCLOOXYGENASE 1, COX-1, PROSTAGLANDIN-ENDOPEROXIDE SYNTHASE 1
SUGAR (NAG-NAG)polymer424.46
B-OCTYLGLUCOSIDEnon-polymer292.45
PROTOPORPHYRIN IX CONTAINING FEnon-polymer616.52
FLURBIPROFENnon-polymer244.32
waterwater18.0130

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains8
Total molecular weight135738.4
Non-Polymers*Number of molecules9
Total molecular weight3183.4
All*Total molecular weight138921.8
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.1 Å)

Cell axes99.400210.300233.100
Cell angles90.0090.0090.00
SpacegroupI 2 2 2
Resolution limits20.00 - 3.10
the highest resolution shell value3.200 - 3.100
R-factor0.186
R-work0.18600
R-free0.22600
RMSD bond length0.013
RMSD bond angle1.700 (23.300*)

Data Collection Statistics

Resolution limits20.00 - 3.10
the highest resolution shell value -
Number of reflections32349
Number of measurements112745*
Rmerge_l_obs0.076
Completeness96.0
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP6.7K*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
11dropenzyme10 (mg/ml)
21dropsodium phosphate20 (mM)
31drop100-200 (mM)
41dropbeta-octyl glucopyranoside0.6 (%(w/v))
51dropflubiprofen0.1 (mM)
61dropPEG40002-4 (%)
71reservoirPEG40004-8 (%)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0005789cellular_componentendoplasmic reticulum membrane
A0016021cellular_componentintegral component of membrane
A0043231cellular_componentintracellular membrane-bounded organelle
A0005634cellular_componentnucleus
A0051213molecular_functiondioxygenase activity
A0020037molecular_functionheme binding
A0046872molecular_functionmetal ion binding
A0004601molecular_functionperoxidase activity
A0004666molecular_functionprostaglandin-endoperoxide synthase activity
A0019371biological_processcyclooxygenase pathway
A0006954biological_processinflammatory response
A0001516biological_processprostaglandin biosynthetic process
A0008217biological_processregulation of blood pressure
A0006979biological_processresponse to oxidative stress
B0005737cellular_componentcytoplasm
B0005789cellular_componentendoplasmic reticulum membrane
B0016021cellular_componentintegral component of membrane
B0043231cellular_componentintracellular membrane-bounded organelle
B0005634cellular_componentnucleus
B0051213molecular_functiondioxygenase activity
B0020037molecular_functionheme binding
B0046872molecular_functionmetal ion binding
B0004601molecular_functionperoxidase activity
B0004666molecular_functionprostaglandin-endoperoxide synthase activity
B0019371biological_processcyclooxygenase pathway
B0006954biological_processinflammatory response
B0001516biological_processprostaglandin biosynthetic process
B0008217biological_processregulation of blood pressure
B0006979biological_processresponse to oxidative stress
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
COA6HYDROPHOBIC CHANNEL RESPONSIBLE FOR CYCLOOGENASE ACTIVITY
ChainResidue
AARG120
ATYR355
ATYR385
ATRP387
AILE523
ASER530

COB6HYDROPHOBIC CHANNEL RESPONSIBLE FOR CYCLOOGENASE ACTIVITY
ChainResidue
BARG120
BTYR355
BTYR385
BTRP387
BILE523
BSER530

POA3HEME POCKET RESPONSIBLE FOR PEROXIDASE ACTIVITY
ChainResidue
AHEM601
AHIS207
AHIS388

POB3HEME POCKET RESPONSIBLE FOR PEROXIDASE ACTIVITY
ChainResidue
BHEM601
BHIS207
BHIS388

AC13BINDING SITE FOR RESIDUE NAG A 661
ChainResidue
ATYR55
AASN68
ANAG662

AC22BINDING SITE FOR RESIDUE NAG A 662
ChainResidue
ATYR38
ANAG661

AC35BINDING SITE FOR RESIDUE NAG A 671
ChainResidue
AGLU140
AASN144
ATYR147
ANAG672
AHOH881

AC44BINDING SITE FOR RESIDUE NAG A 672
ChainResidue
AMET216
ANAG671
BLEU238
BGLU239

AC57BINDING SITE FOR RESIDUE NAG A 681
ChainResidue
ATYR402
AGLN406
AASN410
AMET413
AASP416
ATYR417
ANAG682

AC63BINDING SITE FOR RESIDUE NAG A 682
ChainResidue
AGLN400
AGLN406
ANAG681

AC73BINDING SITE FOR RESIDUE NAG B 661
ChainResidue
BTYR55
BASN68
BNAG662

AC82BINDING SITE FOR RESIDUE NAG B 662
ChainResidue
BTYR38
BNAG661

AC95BINDING SITE FOR RESIDUE NAG B 671
ChainResidue
BGLU140
BASN144
BTYR147
BNAG672
BHOH981

BC14BINDING SITE FOR RESIDUE NAG B 672
ChainResidue
ALEU238
AGLU239
BMET216
BNAG671

BC28BINDING SITE FOR RESIDUE NAG B 681
ChainResidue
AGLN282
BTYR402
BGLN406
BASN410
BMET413
BASP416
BTYR417
BNAG682

BC34BINDING SITE FOR RESIDUE NAG B 682
ChainResidue
BGLN400
BTYR402
BGLN406
BNAG681

BC46BINDING SITE FOR RESIDUE BOG A 1701
ChainResidue
ATHR70
AILE74
ATRP77
BTRP98
BASP101
BPHE102

BC55BINDING SITE FOR RESIDUE BOG A 1702
ChainResidue
ALEU115
AVAL116
AVAL119
AHOH885
AHOH1124

BC64BINDING SITE FOR RESIDUE BOG A 1703
ChainResidue
BPHE102
BTHR106
BPHE107
BILE108

BC75BINDING SITE FOR RESIDUE BOG B 2802
ChainResidue
BLEU115
BVAL116
BVAL119
BARG120
BHOH985

BC82BINDING SITE FOR RESIDUE BOG B 2803
ChainResidue
BGLY96
BLEU99

BC916BINDING SITE FOR RESIDUE HEM A 601
ChainResidue
AALA199
AALA202
AGLN203
AHIS207
APHE210
ALYS211
ATHR212
ALEU295
AASN382
ATYR385
AHIS386
AHIS388
AMET391
AILE444
AVAL447
AASP450

CC116BINDING SITE FOR RESIDUE HEM B 601
ChainResidue
BALA199
BALA202
BGLN203
BHIS207
BPHE210
BLYS211
BTHR212
BLEU295
BASN382
BTYR385
BHIS386
BHIS388
BMET391
BILE444
BVAL447
BASP450

CC212BINDING SITE FOR RESIDUE FLP A 1650
ChainResidue
AVAL116
AARG120
AVAL349
ALEU352
ATYR355
ALEU359
ATYR385
ATRP387
AILE523
AGLY526
AALA527
ASER530

CC311BINDING SITE FOR RESIDUE FLP B 2650
ChainResidue
BARG120
BVAL349
BLEU352
BTYR355
BLEU359
BTYR385
BTRP387
BILE523
BGLY526
BALA527
BSER530

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
NAG_1cqe_A_6623N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
APRO35NAG: N-ACETYL-D-GLUCOSAMINE
ATYR38NAG: N-ACETYL-D-GLUCOSAMINE
ATYR55NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1cqe_A_6616N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ATYR38NAG: N-ACETYL-D-GLUCOSAMINE
APRO40NAG: N-ACETYL-D-GLUCOSAMINE
ATYR55NAG: N-ACETYL-D-GLUCOSAMINE
APRO67-ASN68NAG: N-ACETYL-D-GLUCOSAMINE
ATHR70NAG: N-ACETYL-D-GLUCOSAMINE

BOG_1cqe_A_17015B-OCTYLGLUCOSIDE binding site
ChainResidueligand
ATHR70-PRO72BOG: B-OCTYLGLUCOSIDE
AILE74BOG: B-OCTYLGLUCOSIDE
ATRP77BOG: B-OCTYLGLUCOSIDE

BOG_1cqe_A_17033B-OCTYLGLUCOSIDE binding site
ChainResidueligand
AGLU73-TRP75BOG: B-OCTYLGLUCOSIDE

BOG_1cqe_A_170210B-OCTYLGLUCOSIDE binding site
ChainResidueligand
AILE89BOG: B-OCTYLGLUCOSIDE
ALEU92-LEU93BOG: B-OCTYLGLUCOSIDE
ATRP100BOG: B-OCTYLGLUCOSIDE
ALEU112BOG: B-OCTYLGLUCOSIDE
ALEU115-VAL116BOG: B-OCTYLGLUCOSIDE
AVAL119-ARG120BOG: B-OCTYLGLUCOSIDE
AGLU524BOG: B-OCTYLGLUCOSIDE

FLP_1cqe_A_165019FLURBIPROFEN binding site
ChainResidueligand
AVAL116FLP: FLURBIPROFEN
AARG120FLP: FLURBIPROFEN
ATYR348-VAL349FLP: FLURBIPROFEN
ALEU352-SER353FLP: FLURBIPROFEN
ATYR355FLP: FLURBIPROFEN
ALEU359FLP: FLURBIPROFEN
APHE381FLP: FLURBIPROFEN
ALEU384-TYR385FLP: FLURBIPROFEN
ATRP387FLP: FLURBIPROFEN
APHE518FLP: FLURBIPROFEN
AMET522-ILE523FLP: FLURBIPROFEN
AGLY526-ALA527FLP: FLURBIPROFEN
ASER530-LEU531FLP: FLURBIPROFEN

NAG_1cqe_A_6717N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AGLU140NAG: N-ACETYL-D-GLUCOSAMINE
AASN144NAG: N-ACETYL-D-GLUCOSAMINE
ASER146-TYR147NAG: N-ACETYL-D-GLUCOSAMINE
APHE220NAG: N-ACETYL-D-GLUCOSAMINE
BLEU238NAG: N-ACETYL-D-GLUCOSAMINE
BTYR242NAG: N-ACETYL-D-GLUCOSAMINE

HEM_1cqe_A_60125PROTOPORPHYRIN IX CONTAINING FE binding site
ChainResidueligand
ATYR148HEM: PROTOPORPHYRIN IX CONTAINING FE
AALA199HEM: PROTOPORPHYRIN IX CONTAINING FE
AALA202-GLN203HEM: PROTOPORPHYRIN IX CONTAINING FE
ATHR206-HIS207HEM: PROTOPORPHYRIN IX CONTAINING FE
APHE210-THR212HEM: PROTOPORPHYRIN IX CONTAINING FE
ALEU295HEM: PROTOPORPHYRIN IX CONTAINING FE
AASN382HEM: PROTOPORPHYRIN IX CONTAINING FE
ATYR385-HIS388HEM: PROTOPORPHYRIN IX CONTAINING FE
ALEU390-MET391HEM: PROTOPORPHYRIN IX CONTAINING FE
APHE395HEM: PROTOPORPHYRIN IX CONTAINING FE
ATYR404HEM: PROTOPORPHYRIN IX CONTAINING FE
ALEU408HEM: PROTOPORPHYRIN IX CONTAINING FE
AILE444HEM: PROTOPORPHYRIN IX CONTAINING FE
AHIS446-VAL447HEM: PROTOPORPHYRIN IX CONTAINING FE
AASP450-VAL451HEM: PROTOPORPHYRIN IX CONTAINING FE

NAG_1cqe_A_6725N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AMET216NAG: N-ACETYL-D-GLUCOSAMINE
APHE220NAG: N-ACETYL-D-GLUCOSAMINE
BLEU238-GLU239NAG: N-ACETYL-D-GLUCOSAMINE
BTYR242NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1cqe_B_6717N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ALEU238NAG: N-ACETYL-D-GLUCOSAMINE
ATYR242NAG: N-ACETYL-D-GLUCOSAMINE
BGLU140NAG: N-ACETYL-D-GLUCOSAMINE
BASN144NAG: N-ACETYL-D-GLUCOSAMINE
BSER146-TYR147NAG: N-ACETYL-D-GLUCOSAMINE
BPHE220NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1cqe_B_6725N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ALEU238-GLU239NAG: N-ACETYL-D-GLUCOSAMINE
ATYR242NAG: N-ACETYL-D-GLUCOSAMINE
BMET216NAG: N-ACETYL-D-GLUCOSAMINE
BPHE220NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1cqe_A_6824N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
AGLN400NAG: N-ACETYL-D-GLUCOSAMINE
ATYR402NAG: N-ACETYL-D-GLUCOSAMINE
AGLN406NAG: N-ACETYL-D-GLUCOSAMINE
AASP416NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1cqe_A_6818N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
ATYR402NAG: N-ACETYL-D-GLUCOSAMINE
AGLU405-GLN406NAG: N-ACETYL-D-GLUCOSAMINE
AASN410NAG: N-ACETYL-D-GLUCOSAMINE
ASER412-MET413NAG: N-ACETYL-D-GLUCOSAMINE
AASP416-TYR417NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1cqe_B_6624N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
BVAL33NAG: N-ACETYL-D-GLUCOSAMINE
BPRO35NAG: N-ACETYL-D-GLUCOSAMINE
BTYR38NAG: N-ACETYL-D-GLUCOSAMINE
BTYR55NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1cqe_B_6615N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
BTYR38NAG: N-ACETYL-D-GLUCOSAMINE
BPRO40NAG: N-ACETYL-D-GLUCOSAMINE
BTYR55NAG: N-ACETYL-D-GLUCOSAMINE
BPRO67-ASN68NAG: N-ACETYL-D-GLUCOSAMINE

BOG_1cqe_B_280210B-OCTYLGLUCOSIDE binding site
ChainResidueligand
BILE89BOG: B-OCTYLGLUCOSIDE
BLEU92-LEU93BOG: B-OCTYLGLUCOSIDE
BTRP100BOG: B-OCTYLGLUCOSIDE
BLEU112BOG: B-OCTYLGLUCOSIDE
BLEU115-VAL116BOG: B-OCTYLGLUCOSIDE
BVAL119-ARG120BOG: B-OCTYLGLUCOSIDE
BGLU524BOG: B-OCTYLGLUCOSIDE

BOG_1cqe_B_28037B-OCTYLGLUCOSIDE binding site
ChainResidueligand
BPHE91-LEU92BOG: B-OCTYLGLUCOSIDE
BHIS95-GLY96BOG: B-OCTYLGLUCOSIDE
BTRP98-TRP100BOG: B-OCTYLGLUCOSIDE

FLP_1cqe_B_265019FLURBIPROFEN binding site
ChainResidueligand
BVAL116FLP: FLURBIPROFEN
BARG120FLP: FLURBIPROFEN
BTYR348-VAL349FLP: FLURBIPROFEN
BLEU352-SER353FLP: FLURBIPROFEN
BTYR355FLP: FLURBIPROFEN
BLEU359FLP: FLURBIPROFEN
BPHE381FLP: FLURBIPROFEN
BLEU384-TYR385FLP: FLURBIPROFEN
BTRP387FLP: FLURBIPROFEN
BPHE518FLP: FLURBIPROFEN
BMET522-ILE523FLP: FLURBIPROFEN
BGLY526-ALA527FLP: FLURBIPROFEN
BSER530-LEU531FLP: FLURBIPROFEN

HEM_1cqe_B_60126PROTOPORPHYRIN IX CONTAINING FE binding site
ChainResidueligand
BTYR148HEM: PROTOPORPHYRIN IX CONTAINING FE
BALA199HEM: PROTOPORPHYRIN IX CONTAINING FE
BALA202-GLN203HEM: PROTOPORPHYRIN IX CONTAINING FE
BTHR206-HIS207HEM: PROTOPORPHYRIN IX CONTAINING FE
BPHE210-THR212HEM: PROTOPORPHYRIN IX CONTAINING FE
BLEU294-LEU295HEM: PROTOPORPHYRIN IX CONTAINING FE
BASN382HEM: PROTOPORPHYRIN IX CONTAINING FE
BTYR385-HIS388HEM: PROTOPORPHYRIN IX CONTAINING FE
BLEU390-MET391HEM: PROTOPORPHYRIN IX CONTAINING FE
BPHE395HEM: PROTOPORPHYRIN IX CONTAINING FE
BTYR404HEM: PROTOPORPHYRIN IX CONTAINING FE
BLEU408HEM: PROTOPORPHYRIN IX CONTAINING FE
BILE444HEM: PROTOPORPHYRIN IX CONTAINING FE
BHIS446-VAL447HEM: PROTOPORPHYRIN IX CONTAINING FE
BASP450-VAL451HEM: PROTOPORPHYRIN IX CONTAINING FE

NAG_1cqe_B_6824N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
BGLN400NAG: N-ACETYL-D-GLUCOSAMINE
BTYR402NAG: N-ACETYL-D-GLUCOSAMINE
BGLN406NAG: N-ACETYL-D-GLUCOSAMINE
BASP416NAG: N-ACETYL-D-GLUCOSAMINE

NAG_1cqe_B_6818N-ACETYL-D-GLUCOSAMINE binding site
ChainResidueligand
BTYR402NAG: N-ACETYL-D-GLUCOSAMINE
BGLU405-GLN406NAG: N-ACETYL-D-GLUCOSAMINE
BASN410NAG: N-ACETYL-D-GLUCOSAMINE
BSER412-MET413NAG: N-ACETYL-D-GLUCOSAMINE
BASP416-TYR417NAG: N-ACETYL-D-GLUCOSAMINE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11For cyclooxygenase activity.
ChainResidueDetails
ATYR365

SWS_FT_FI21Proton acceptor.
ChainResidueDetails
AHIS187

SWS_FT_FI71For cyclooxygenase activity.
ChainResidueDetails
BTYR365

SWS_FT_FI81Proton acceptor.
ChainResidueDetails
BHIS187

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
CSA11Annotated By Reference To The Literature 1mhl
ChainResidueDetails
AVAL291

CSA21Annotated By Reference To The Literature 1mhl
ChainResidueDetails
BVAL291

CSA33Annotated By Reference To The Literature 1mhl
ChainResidueDetails
AHIS207
ATYR385
AGLN203

CSA43Annotated By Reference To The Literature 1mhl
ChainResidueDetails
BHIS207
BTYR385
BGLN203

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Catalytic Information from CATRES

site_idNumber of ResiduesDetails
extCATRES13Mapped from 5cox to 1cqe using BLAST. All catalytic residues present. Original details record follows: a catalytic site defined by CATRES, Medline 20269363, 20290850, 20463516, 91056037, 91177862, 97407953
ChainResidueDetails
AGLN203activates substrate. assist in peroxide formation
AHIS207activates substrate. assist in peroxide formation
ATYR385radical. Radical

> Sequence Neighbor

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