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

Experimental method:X-RAY DIFFRACTION (1.75 Å)

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
A0006635biological_processfatty acid beta-oxidation
A0051289biological_processprotein homotetramerization
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
B0006635biological_processfatty acid beta-oxidation
B0051289biological_processprotein homotetramerization
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
C0006635biological_processfatty acid beta-oxidation
C0051289biological_processprotein homotetramerization
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
D0006635biological_processfatty acid beta-oxidation
D0051289biological_processprotein homotetramerization
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC117BINDING SITE FOR RESIDUE HXC A1330
ChainResidue
AARG119
AALA146
AGLY147
AASN148
APHE149
ASER157
AASN159
ATHR163
ATHR197
ATYR199
ASER210
ANAP1329
AHOH2075
AHOH2132
AHOH2134
AHOH2137
DGLU326

AC215BINDING SITE FOR RESIDUE HXC B1331
ChainResidue
BARG91
BARG119
BGLY147
BASN148
BPHE149
BSER157
BASN159
BALA160
BTYR199
BNAP1330
BHOH2069
BHOH2147
BHOH2148
CGLU326
CHOH2126

AC317BINDING SITE FOR RESIDUE HXC C1330
ChainResidue
BGLU310
BGLU326
CALA146
CGLY147
CASN148
CPHE149
CSER157
CASN159
CTHR163
CTHR197
CTYR199
CNAP1329
CHOH2047
CHOH2079
CHOH2128
CHOH2130
CHOH2131

AC414BINDING SITE FOR RESIDUE HXC D1329
ChainResidue
AGLU326
DARG91
DALA146
DGLY147
DASN148
DPHE149
DSER157
DASN159
DTHR163
DILE164
DLYS214
DNAP1328
DHOH2161
DHOH2162

AC525BINDING SITE FOR RESIDUE NAP A1329
ChainResidue
AGLY66
ATHR69
AGLY70
ALEU71
ASER90
AARG91
ALYS92
ACYS116
AASP117
AVAL118
AASN144
AALA145
AALA146
AILE195
ATHR196
ALYS214
APRO240
AGLY241
APRO242
AILE243
AHXC1330
AHOH2129
AHOH2130
AHOH2131
AHOH2132

AC626BINDING SITE FOR RESIDUE NAP B1330
ChainResidue
BGLY66
BTHR69
BGLY70
BLEU71
BSER90
BARG91
BLYS92
BCYS116
BASP117
BVAL118
BARG119
BASN144
BALA145
BALA146
BILE167
BILE195
BTHR196
BLYS214
BPRO240
BGLY241
BPRO242
BILE243
BHXC1331
BHOH2060
BHOH2144
BHOH2146

AC727BINDING SITE FOR RESIDUE NAP C1329
ChainResidue
CGLY66
CTHR69
CGLY70
CLEU71
CSER90
CARG91
CLYS92
CCYS116
CASP117
CVAL118
CASN144
CALA145
CALA146
CILE195
CTHR196
CLYS214
CPRO240
CGLY241
CPRO242
CILE243
CTHR245
CHXC1330
CHOH2009
CHOH2010
CHOH2127
CHOH2128
CHOH2129

AC826BINDING SITE FOR RESIDUE NAP D1328
ChainResidue
DGLY66
DTHR69
DGLY70
DLEU71
DSER90
DARG91
DLYS92
DCYS116
DASP117
DVAL118
DASN144
DALA145
DALA146
DILE195
DTHR196
DLYS214
DPRO240
DGLY241
DPRO242
DILE243
DHXC1329
DHOH2033
DHOH2156
DHOH2157
DHOH2158
DHOH2159

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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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