1W6U

STRUCTURE OF HUMAN DECR TERNARY COMPLEX

> Summary

Summary for 1W6U

Related1W73 1W8D
Descriptor2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSOR (E.C.1.3.1.34)
Functional Keywordsdienoyl coa-reductase, short chain dehydrogenase, beta-oxidation, nadp, oxidoreductase, reductase
Biological sourceHOMO SAPIENS (HUMAN)
Cellular locationMitochondrion Q16698
Total number of polymer chains4
Total molecular weight135697.65
Authors
Alphey, M.S.,Byres, E.,Li, D.,Hunter, W.N. (deposition date: 2004-08-24, release date: 2004-10-28, modification date: 2009-02-24)
Primary citation
Alphey, M.S.,Yu, W.,Byres, E.,Li, D.,Hunter, W.N.
Structure and Reactivity of Human Mitochondrial 2,4-Dienoyl-Coa Reductase: Enzyme-Ligand Interactions in a Distinctive Short-Chain Reductase Active Site
J.Biol.Chem., 280:3068-, 2005
PubMed: 15531764
DOI: 10.1074/JBC.M411069200
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.75 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.26560.2%8.6%17.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1w6u
no rotation
Molmil generated image of 1w6u
rotated about x axis by 90°
Molmil generated image of 1w6u
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, D2,4-DIENOYL-COA REDUCTASE, MITOCHONDRIAL PRECURSORpolymer30232315.34
UniProt (Q16698)
Pfam (PF13561)
HOMO SAPIENS (HUMAN)@PDBj2,4-DIENOYL-COA REDUCTASE [NADPH], 4-ENOYL-COA REDUCTASE [NADPH]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATEnon-polymer743.44
HEXANOYL-COENZYME Anon-polymer865.74
waterwater18.0580

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight129261.3
Non-Polymers*Number of molecules8
Total molecular weight6436.4
All*Total molecular weight135697.6
*Water molecules are not included.

> Experimental details

Refinement Statistics

Cell axes63.281131.65870.849
Cell angles90.0092.6490.00
SpacegroupP 1 21 1
Resolution limits70.71 - 1.75
the highest resolution shell value1.800 - 1.750
R-factor0.229
R-work0.22700
the highest resolution shell value0.357
R-free0.26800
the highest resolution shell value0.365
RMSD bond length0.007
RMSD bond angle1.155

Data Collection Statistics

Resolution limits30.00 - 1.75
the highest resolution shell value -
Number of reflections110749
Rmerge_l_obs0.050
the highest resolution shell value0.590
Completeness95.5
Redundancy3.6
the highest resolution shell value3.3
I/sigma(I)2

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
17.4

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0005737cellular_componentcytoplasm
A0070062cellular_componentextracellular exosome
A0005759cellular_componentmitochondrial matrix
A0005739cellular_componentmitochondrion
A0005654cellular_componentnucleoplasm
A0005634cellular_componentnucleus
A0008670molecular_function2,4-dienoyl-CoA reductase (NADPH) activity
A0070402molecular_functionNADPH binding
A0016651molecular_functionoxidoreductase activity, acting on NAD(P)H
A0044255biological_processcellular lipid metabolic process
A0006635biological_processfatty acid beta-oxidation
A0051289biological_processprotein homotetramerization
A0044281biological_processsmall molecule metabolic process
B0005737cellular_componentcytoplasm
B0070062cellular_componentextracellular exosome
B0005759cellular_componentmitochondrial matrix
B0005739cellular_componentmitochondrion
B0005654cellular_componentnucleoplasm
B0005634cellular_componentnucleus
B0008670molecular_function2,4-dienoyl-CoA reductase (NADPH) activity
B0070402molecular_functionNADPH binding
B0016651molecular_functionoxidoreductase activity, acting on NAD(P)H
B0044255biological_processcellular lipid metabolic process
B0006635biological_processfatty acid beta-oxidation
B0051289biological_processprotein homotetramerization
B0044281biological_processsmall molecule metabolic process
C0005737cellular_componentcytoplasm
C0070062cellular_componentextracellular exosome
C0005759cellular_componentmitochondrial matrix
C0005739cellular_componentmitochondrion
C0005654cellular_componentnucleoplasm
C0005634cellular_componentnucleus
C0008670molecular_function2,4-dienoyl-CoA reductase (NADPH) activity
C0070402molecular_functionNADPH binding
C0016651molecular_functionoxidoreductase activity, acting on NAD(P)H
C0044255biological_processcellular lipid metabolic process
C0006635biological_processfatty acid beta-oxidation
C0051289biological_processprotein homotetramerization
C0044281biological_processsmall molecule metabolic process
D0005737cellular_componentcytoplasm
D0070062cellular_componentextracellular exosome
D0005759cellular_componentmitochondrial matrix
D0005739cellular_componentmitochondrion
D0005654cellular_componentnucleoplasm
D0005634cellular_componentnucleus
D0008670molecular_function2,4-dienoyl-CoA reductase (NADPH) activity
D0070402molecular_functionNADPH binding
D0016651molecular_functionoxidoreductase activity, acting on NAD(P)H
D0044255biological_processcellular lipid metabolic process
D0006635biological_processfatty acid beta-oxidation
D0051289biological_processprotein homotetramerization
D0044281biological_processsmall molecule metabolic process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC117BINDING SITE FOR RESIDUE HXC A1330
ChainResidue
AARG86
AALA113
AGLY114
AASN115
APHE116
ASER124
AASN126
ATHR130
ATHR164
ATYR166
ASER177
ANAP
AHOH
AHOH
AHOH
AHOH
DGLU293

AC215BINDING SITE FOR RESIDUE HXC B1331
ChainResidue
BARG58
BARG86
BGLY114
BASN115
BPHE116
BSER124
BASN126
BALA127
BTYR166
BNAP
BHOH
BHOH
BHOH
CGLU293
CHOH

AC317BINDING SITE FOR RESIDUE HXC C1330
ChainResidue
BGLU277
BGLU293
CALA113
CGLY114
CASN115
CPHE116
CSER124
CASN126
CTHR130
CTHR164
CTYR166
CNAP
CHOH
CHOH
CHOH
CHOH
CHOH

AC414BINDING SITE FOR RESIDUE HXC D1329
ChainResidue
AGLU293
DARG58
DALA113
DGLY114
DASN115
DPHE116
DSER124
DASN126
DTHR130
DILE131
DLYS181
DNAP
DHOH
DHOH

AC525BINDING SITE FOR RESIDUE NAP A1329
ChainResidue
AGLY33
ATHR36
AGLY37
ALEU38
ASER57
AARG58
ALYS59
ACYS83
AASP84
AVAL85
AASN111
AALA112
AALA113
AILE162
ATHR163
ALYS181
APRO207
AGLY208
APRO209
AILE210
AHXC
AHOH
AHOH
AHOH
AHOH

AC626BINDING SITE FOR RESIDUE NAP B1330
ChainResidue
BGLY33
BTHR36
BGLY37
BLEU38
BSER57
BARG58
BLYS59
BCYS83
BASP84
BVAL85
BARG86
BASN111
BALA112
BALA113
BILE134
BILE162
BTHR163
BLYS181
BPRO207
BGLY208
BPRO209
BILE210
BHXC
BHOH
BHOH
BHOH

AC727BINDING SITE FOR RESIDUE NAP C1329
ChainResidue
CGLY33
CTHR36
CGLY37
CLEU38
CSER57
CARG58
CLYS59
CCYS83
CASP84
CVAL85
CASN111
CALA112
CALA113
CILE162
CTHR163
CLYS181
CPRO207
CGLY208
CPRO209
CILE210
CTHR212
CHXC
CHOH
CHOH
CHOH
CHOH
CHOH

AC826BINDING SITE FOR RESIDUE NAP D1328
ChainResidue
DGLY33
DTHR36
DGLY37
DLEU38
DSER57
DARG58
DLYS59
DCYS83
DASP84
DVAL85
DASN111
DALA112
DALA113
DILE162
DTHR163
DLYS181
DPRO207
DGLY208
DPRO209
DILE210
DHXC
DHOH
DHOH
DHOH
DHOH
DHOH

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

site_idNumber of ResiduesDetails
NAP_1w6u_A_132928NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE binding site
ChainResidueligand
AGLY66-GLY72NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AALA89-LYS92NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ACYS116-ARG119NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AASN144-ALA146NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AILE167NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AILE195-THR197NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ALYS214NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
APRO240-ILE243NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ATHR245NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

HXC_1w6u_A_133024HEXANOYL-COENZYME A binding site
ChainResidueligand
AARG91HXC: HEXANOYL-COENZYME A
AARG119HXC: HEXANOYL-COENZYME A
AALA146-PHE149HXC: HEXANOYL-COENZYME A
ASER151HXC: HEXANOYL-COENZYME A
ALEU156-SER157HXC: HEXANOYL-COENZYME A
AASN159-ALA160HXC: HEXANOYL-COENZYME A
ATHR163-ILE164HXC: HEXANOYL-COENZYME A
AILE167HXC: HEXANOYL-COENZYME A
ATHR197HXC: HEXANOYL-COENZYME A
ATYR199HXC: HEXANOYL-COENZYME A
ASER210HXC: HEXANOYL-COENZYME A
ALYS214HXC: HEXANOYL-COENZYME A
AGLY241-PRO242HXC: HEXANOYL-COENZYME A
AMET262HXC: HEXANOYL-COENZYME A
DGLU310-PHE311HXC: HEXANOYL-COENZYME A
DGLU326HXC: HEXANOYL-COENZYME A

HXC_1w6u_D_132921HEXANOYL-COENZYME A binding site
ChainResidueligand
APHE311HXC: HEXANOYL-COENZYME A
AGLU326HXC: HEXANOYL-COENZYME A
DARG91HXC: HEXANOYL-COENZYME A
DARG119HXC: HEXANOYL-COENZYME A
DALA146-PHE149HXC: HEXANOYL-COENZYME A
DSER151HXC: HEXANOYL-COENZYME A
DARG155-SER157HXC: HEXANOYL-COENZYME A
DASN159-ALA160HXC: HEXANOYL-COENZYME A
DTHR163-ILE164HXC: HEXANOYL-COENZYME A
DILE167HXC: HEXANOYL-COENZYME A
DTHR197HXC: HEXANOYL-COENZYME A
DTYR199HXC: HEXANOYL-COENZYME A
DSER210HXC: HEXANOYL-COENZYME A
DLYS214HXC: HEXANOYL-COENZYME A

NAP_1w6u_B_133028NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE binding site
ChainResidueligand
BGLY66-GLY72NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BALA89-LYS92NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BCYS116-ARG119NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BASN144-GLY147NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BILE167NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BILE195-THR197NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BLYS214NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
BPRO240-ILE243NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

HXC_1w6u_B_133122HEXANOYL-COENZYME A binding site
ChainResidueligand
BARG91HXC: HEXANOYL-COENZYME A
BARG119HXC: HEXANOYL-COENZYME A
BALA146-SER151HXC: HEXANOYL-COENZYME A
BARG155-SER157HXC: HEXANOYL-COENZYME A
BASN159-ALA160HXC: HEXANOYL-COENZYME A
BTHR163-ILE164HXC: HEXANOYL-COENZYME A
BILE167HXC: HEXANOYL-COENZYME A
BTHR197HXC: HEXANOYL-COENZYME A
BTYR199HXC: HEXANOYL-COENZYME A
BSER210HXC: HEXANOYL-COENZYME A
BLYS214HXC: HEXANOYL-COENZYME A
CPHE311HXC: HEXANOYL-COENZYME A
CGLU326HXC: HEXANOYL-COENZYME A

HXC_1w6u_C_133027HEXANOYL-COENZYME A binding site
ChainResidueligand
BGLU310-PHE311HXC: HEXANOYL-COENZYME A
BGLU326HXC: HEXANOYL-COENZYME A
BILE329HXC: HEXANOYL-COENZYME A
CARG91HXC: HEXANOYL-COENZYME A
CARG119HXC: HEXANOYL-COENZYME A
CALA146-PHE149HXC: HEXANOYL-COENZYME A
CSER151HXC: HEXANOYL-COENZYME A
CARG155-SER157HXC: HEXANOYL-COENZYME A
CASN159-ALA160HXC: HEXANOYL-COENZYME A
CTHR163-ILE164HXC: HEXANOYL-COENZYME A
CTHR196-THR197HXC: HEXANOYL-COENZYME A
CTYR199HXC: HEXANOYL-COENZYME A
CSER210HXC: HEXANOYL-COENZYME A
CLYS214HXC: HEXANOYL-COENZYME A
CGLY241-PRO242HXC: HEXANOYL-COENZYME A
CGLY247-ALA248HXC: HEXANOYL-COENZYME A

NAP_1w6u_C_132930NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE binding site
ChainResidueligand
CGLY66-GLY72NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CALA89-LYS92NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CCYS116-ARG119NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CASN144-GLY147NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CILE167NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CILE195-THR197NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CLYS214NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CPRO240-ILE243NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CTHR245NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
CGLY247NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

NAP_1w6u_D_132828NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE binding site
ChainResidueligand
DGLY66-GLY72NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DALA89-LYS92NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DCYS116-ARG119NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DASN144-ALA146NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DILE167NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DILE195-THR197NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DLYS214NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DPRO240-ILE243NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
DTHR245NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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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_FI11Proton acceptor (Probable).
ChainResidueDetails
ATYR166

SWS_FT_FI21NAD.
ChainResidueDetails
ALYS181

SWS_FT_FI31Substrate.
ChainResidueDetails
ASER124

SWS_FT_FI41NADP.
ChainResidueDetails
ANA*

SWS_FT_FI51Proton acceptor (Probable).
ChainResidueDetails
BTYR166

SWS_FT_FI61NAD.
ChainResidueDetails
BLYS181

SWS_FT_FI71Substrate.
ChainResidueDetails
BSER124

SWS_FT_FI81NADP.
ChainResidueDetails
BNA*

SWS_FT_FI91Proton acceptor (Probable).
ChainResidueDetails
CTYR166

SWS_FT_FI101NAD.
ChainResidueDetails
CLYS181

SWS_FT_FI111Substrate.
ChainResidueDetails
CSER124

SWS_FT_FI121NADP.
ChainResidueDetails
CNA*

SWS_FT_FI131Proton acceptor (Probable).
ChainResidueDetails
DTYR166

SWS_FT_FI141NAD.
ChainResidueDetails
DLYS181

SWS_FT_FI151Substrate.
ChainResidueDetails
DSER124

SWS_FT_FI161NADP.
ChainResidueDetails
DNA*

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
CSA12Annotated By Reference To The Literature 1qsg
ChainResidueDetails
AVAL207
ALYS214

CSA22Annotated By Reference To The Literature 1qsg
ChainResidueDetails
BVAL207
BLYS214

CSA32Annotated By Reference To The Literature 1qsg
ChainResidueDetails
CVAL207
CLYS214

CSA42Annotated By Reference To The Literature 1qsg
ChainResidueDetails
DVAL207
DLYS214

CSA52Annotated By Reference To The Literature 1qsg
ChainResidueDetails
ALYS214
ASER210

CSA62Annotated By Reference To The Literature 1qsg
ChainResidueDetails
BLYS214
BSER210

CSA72Annotated By Reference To The Literature 1qsg
ChainResidueDetails
CLYS214
CSER210

CSA82Annotated By Reference To The Literature 1qsg
ChainResidueDetails
DLYS214
DSER210

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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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