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3N7U

NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex with NAD and azide

Functional Information from GO Data
ChainGOidnamespacecontents
A0005739cellular_componentmitochondrion
A0005829cellular_componentcytosol
A0008863molecular_functionformate dehydrogenase (NAD+) activity
A0009507cellular_componentchloroplast
A0009536cellular_componentplastid
A0009579cellular_componentthylakoid
A0016491molecular_functionoxidoreductase activity
A0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A0042183biological_processformate catabolic process
A0051287molecular_functionNAD binding
B0005739cellular_componentmitochondrion
B0005829cellular_componentcytosol
B0008863molecular_functionformate dehydrogenase (NAD+) activity
B0009507cellular_componentchloroplast
B0009536cellular_componentplastid
B0009579cellular_componentthylakoid
B0016491molecular_functionoxidoreductase activity
B0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B0042183biological_processformate catabolic process
B0051287molecular_functionNAD binding
C0005739cellular_componentmitochondrion
C0005829cellular_componentcytosol
C0008863molecular_functionformate dehydrogenase (NAD+) activity
C0009507cellular_componentchloroplast
C0009536cellular_componentplastid
C0009579cellular_componentthylakoid
C0016491molecular_functionoxidoreductase activity
C0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C0042183biological_processformate catabolic process
C0051287molecular_functionNAD binding
D0005739cellular_componentmitochondrion
D0005829cellular_componentcytosol
D0008863molecular_functionformate dehydrogenase (NAD+) activity
D0009507cellular_componentchloroplast
D0009536cellular_componentplastid
D0009579cellular_componentthylakoid
D0016491molecular_functionoxidoreductase activity
D0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D0042183biological_processformate catabolic process
D0051287molecular_functionNAD binding
E0005739cellular_componentmitochondrion
E0005829cellular_componentcytosol
E0008863molecular_functionformate dehydrogenase (NAD+) activity
E0009507cellular_componentchloroplast
E0009536cellular_componentplastid
E0009579cellular_componentthylakoid
E0016491molecular_functionoxidoreductase activity
E0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
E0042183biological_processformate catabolic process
E0051287molecular_functionNAD binding
F0005739cellular_componentmitochondrion
F0005829cellular_componentcytosol
F0008863molecular_functionformate dehydrogenase (NAD+) activity
F0009507cellular_componentchloroplast
F0009536cellular_componentplastid
F0009579cellular_componentthylakoid
F0016491molecular_functionoxidoreductase activity
F0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F0042183biological_processformate catabolic process
F0051287molecular_functionNAD binding
G0005739cellular_componentmitochondrion
G0005829cellular_componentcytosol
G0008863molecular_functionformate dehydrogenase (NAD+) activity
G0009507cellular_componentchloroplast
G0009536cellular_componentplastid
G0009579cellular_componentthylakoid
G0016491molecular_functionoxidoreductase activity
G0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
G0042183biological_processformate catabolic process
G0051287molecular_functionNAD binding
H0005739cellular_componentmitochondrion
H0005829cellular_componentcytosol
H0008863molecular_functionformate dehydrogenase (NAD+) activity
H0009507cellular_componentchloroplast
H0009536cellular_componentplastid
H0009579cellular_componentthylakoid
H0016491molecular_functionoxidoreductase activity
H0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
H0042183biological_processformate catabolic process
H0051287molecular_functionNAD binding
I0005739cellular_componentmitochondrion
I0005829cellular_componentcytosol
I0008863molecular_functionformate dehydrogenase (NAD+) activity
I0009507cellular_componentchloroplast
I0009536cellular_componentplastid
I0009579cellular_componentthylakoid
I0016491molecular_functionoxidoreductase activity
I0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
I0042183biological_processformate catabolic process
I0051287molecular_functionNAD binding
J0005739cellular_componentmitochondrion
J0005829cellular_componentcytosol
J0008863molecular_functionformate dehydrogenase (NAD+) activity
J0009507cellular_componentchloroplast
J0009536cellular_componentplastid
J0009579cellular_componentthylakoid
J0016491molecular_functionoxidoreductase activity
J0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
J0042183biological_processformate catabolic process
J0051287molecular_functionNAD binding
K0005739cellular_componentmitochondrion
K0005829cellular_componentcytosol
K0008863molecular_functionformate dehydrogenase (NAD+) activity
K0009507cellular_componentchloroplast
K0009536cellular_componentplastid
K0009579cellular_componentthylakoid
K0016491molecular_functionoxidoreductase activity
K0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
K0042183biological_processformate catabolic process
K0051287molecular_functionNAD binding
L0005739cellular_componentmitochondrion
L0005829cellular_componentcytosol
L0008863molecular_functionformate dehydrogenase (NAD+) activity
L0009507cellular_componentchloroplast
L0009536cellular_componentplastid
L0009579cellular_componentthylakoid
L0016491molecular_functionoxidoreductase activity
L0016616molecular_functionoxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
L0042183biological_processformate catabolic process
L0051287molecular_functionNAD binding
Functional Information from PDB Data
site_idAC1
Number of Residues32
DetailsBINDING SITE FOR RESIDUE NAD A 401
ChainResidue
AILE122
AMET255
APRO256
AASN282
AALA283
AARG284
AASP308
AHIS332
ASER334
AGLY335
AGLN376
AASN146
ATYR377
AHOH383
AAZI403
AHOH585
AHOH586
AHOH588
AHOH589
AHOH590
AHOH591
AHOH592
AVAL147
AHOH593
AHOH595
AHOH596
AVAL150
AGLY200
AARG201
AILE202
AASP221
AARG222

site_idAC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI A 403
ChainResidue
APRO97
APHE98
AILE122
AASN146
AARG284
AHIS332
ANAD401

site_idAC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 A 1
ChainResidue
AARG354
APRO362

site_idAC4
Number of Residues34
DetailsBINDING SITE FOR RESIDUE NAD B 401
ChainResidue
BHOH14
BILE122
BASN146
BVAL147
BVAL150
BGLY200
BARG201
BILE202
BASP221
BARG222
BMET255
BPRO256
BASN282
BALA283
BARG284
BASP308
BVAL309
BHIS332
BSER334
BGLY335
BGLN376
BTYR377
BAZI403
BHOH413
BHOH588
BHOH589
BHOH591
BHOH592
BHOH593
BHOH594
BHOH595
BHOH596
BHOH597
BHOH598

site_idAC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI B 403
ChainResidue
BPRO97
BPHE98
BILE122
BASN146
BARG284
BHIS332
BNAD401

site_idAC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 B 2
ChainResidue
BHOH27
BARG354
BPRO362

site_idAC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL B 16
ChainResidue
BTYR184
BARG185
BASN326
BHOH611
BHOH687

site_idAC8
Number of Residues33
DetailsBINDING SITE FOR RESIDUE NAD C 401
ChainResidue
CMET255
CPRO256
CASN282
CALA283
CARG284
CASP308
CVAL309
CHIS332
CSER334
CGLY335
CGLN376
CAZI403
CHOH430
CHOH548
CHOH549
CHOH551
CHOH552
CHOH553
CHOH554
CHOH555
CHOH557
CHOH558
CHOH559
CHOH667
CILE122
CASN146
CVAL147
CVAL150
CGLY200
CARG201
CILE202
CASP221
CARG222

site_idAC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI C 403
ChainResidue
CPRO97
CPHE98
CILE122
CASN146
CARG284
CHIS332
CNAD401

site_idBC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 C 3
ChainResidue
CARG354
CPRO362
CHOH665

site_idBC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL C 10
ChainResidue
CARG378
CHOH688
EARG60
EASP61

site_idBC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE GOL C 17
ChainResidue
CTYR184
CARG185
CASN326

site_idBC4
Number of Residues32
DetailsBINDING SITE FOR RESIDUE NAD D 401
ChainResidue
DHOH3
DHOH6
DILE122
DASN146
DVAL147
DVAL150
DGLY200
DARG201
DILE202
DASP221
DARG222
DMET255
DPRO256
DASN282
DALA283
DARG284
DASP308
DHIS332
DSER334
DGLY335
DGLN376
DAZI403
DHOH562
DHOH563
DHOH565
DHOH566
DHOH567
DHOH568
DHOH569
DHOH570
DHOH571
DHOH649

site_idBC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI D 403
ChainResidue
DPRO97
DPHE98
DILE122
DASN146
DARG284
DHIS332
DNAD401

site_idBC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE SO4 D 4
ChainResidue
DARG354
DPRO362
DHOH670

site_idBC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE GOL D 11
ChainResidue
DARG378
JHOH11
JASP61

site_idBC8
Number of Residues3
DetailsBINDING SITE FOR RESIDUE GOL D 18
ChainResidue
DTYR184
DARG185
DASN326

site_idBC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL D 22
ChainResidue
DASN170
DLYS174
DHOH506
DHOH579

site_idCC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE GOL D 25
ChainResidue
DHIS126
DHOH391

site_idCC2
Number of Residues32
DetailsBINDING SITE FOR RESIDUE NAD E 401
ChainResidue
EASN146
EVAL147
EVAL150
EGLY200
EARG201
EILE202
EASP221
EARG222
EMET255
EPRO256
EASN282
EALA283
EARG284
EASP308
EVAL309
EHIS332
ESER334
EGLY335
EGLN376
EAZI403
EHOH565
EHOH566
EHOH568
EHOH569
EHOH570
EHOH571
EHOH572
EHOH574
EHOH575
EHOH654
HHOH509
HHOH510

site_idCC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE AZI E 403
ChainResidue
EPRO97
EPHE98
EGLY121
EILE122
EASN146
EARG284
EHIS332
ENAD401

site_idCC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL E 379
ChainResidue
EHOH22
EASP125
EHIS126
EASP128
EHOH513
EHOH514

site_idCC5
Number of Residues33
DetailsBINDING SITE FOR RESIDUE NAD F 401
ChainResidue
FASN146
FVAL147
FVAL150
FGLY200
FARG201
FILE202
FHIS220
FASP221
FARG222
FMET255
FPRO256
FASN282
FALA283
FARG284
FASP308
FVAL309
FHIS332
FSER334
FGLY335
FGLN376
FAZI403
FHOH405
FHOH410
FHOH534
FHOH535
FHOH537
FHOH538
FHOH539
FHOH540
FHOH541
FHOH542
FHOH543
FHOH544

site_idCC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI F 403
ChainResidue
FPRO97
FPHE98
FILE122
FASN146
FARG284
FHIS332
FNAD401

site_idCC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 F 20
ChainResidue
FARG354
FPRO362
FHOH402
FHOH631

site_idCC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL F 26
ChainResidue
FTYR102
FVAL103
FHIS126
FASP128
FHOH508
FHOH545
FHOH614

site_idCC9
Number of Residues33
DetailsBINDING SITE FOR RESIDUE NAD G 401
ChainResidue
GHOH21
GPHE98
GILE122
GASN146
GVAL147
GVAL150
GGLY200
GARG201
GILE202
GASP221
GARG222
GMET255
GPRO256
GASN282
GALA283
GARG284
GASP308
GHIS332
GSER334
GGLY335
GGLN376
GHOH402
GAZI403
GHOH479
GHOH543
GHOH544
GHOH546
GHOH547
GHOH548
GHOH549
GHOH551
IHOH502
IHOH503

site_idDC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI G 403
ChainResidue
GPRO97
GPHE98
GILE122
GASN146
GARG284
GHIS332
GNAD401

site_idDC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 G 5
ChainResidue
GTHR138
GLYS369
GASP370
GHOH456
GHOH627

site_idDC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL G 9
ChainResidue
BARG378
GARG60
GASP61
GHOH498
GHOH532

site_idDC4
Number of Residues33
DetailsBINDING SITE FOR RESIDUE NAD H 401
ChainResidue
HPHE98
HILE122
HASN146
HVAL147
HVAL150
HGLY200
HARG201
HILE202
HASP221
HARG222
HMET255
HPRO256
HASN282
HALA283
HARG284
HASP308
HHIS332
HSER334
HGLY335
HGLN376
HAZI403
HHOH543
HHOH544
HHOH546
HHOH547
HHOH548
HHOH549
HHOH550
HHOH551
HHOH553
HHOH554
HHOH555
HHOH625

site_idDC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI H 403
ChainResidue
HPRO97
HPHE98
HILE122
HASN146
HARG284
HHIS332
HNAD401

site_idDC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 H 6
ChainResidue
HGOL12
HLYS115
HTHR138
HLYS369
HHOH558

site_idDC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL H 12
ChainResidue
HSO46
HTYR355
HGLU359
HPHE361
HTYR366
HHOH391
HHOH482

site_idDC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL H 27
ChainResidue
HHOH17
HTYR102
HTHR104
HHIS126
HASP128
HHOH556

site_idDC9
Number of Residues32
DetailsBINDING SITE FOR RESIDUE NAD I 401
ChainResidue
IILE122
IASN146
IVAL147
IVAL150
IGLY200
IARG201
IILE202
IASP221
IARG222
IMET255
IPRO256
IASN282
IALA283
IARG284
IASP308
IVAL309
IHIS332
ISER334
IGLY335
IGLN376
IAZI403
IHOH521
IHOH522
IHOH524
IHOH525
IHOH526
IHOH527
IHOH528
IHOH529
IHOH531
IHOH532
IHOH613

site_idEC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI I 403
ChainResidue
IPRO97
IPHE98
IILE122
IASN146
IARG284
IHIS332
INAD401

site_idEC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 I 7
ChainResidue
IGOL13
ILYS115
ITHR138
ILYS369
IHOH536

site_idEC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL I 13
ChainResidue
ISO47
IARG354
ITYR355
IGLU359
IPHE361
ITYR366
IHOH594

site_idEC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL I 19
ChainResidue
ILEU57
ILEU342
IALA346
IHOH513

site_idEC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL I 23
ChainResidue
ITYR102
IHIS126
IASP128
IHOH418
IHOH490
IHOH534

site_idEC6
Number of Residues31
DetailsBINDING SITE FOR RESIDUE NAD J 401
ChainResidue
JHOH18
JPHE98
JILE122
JASN146
JVAL147
JVAL150
JGLY200
JARG201
JILE202
JASP221
JARG222
JMET255
JPRO256
JASN282
JARG284
JASP308
JVAL309
JHIS332
JSER334
JGLY335
JGLN376
JAZI403
JHOH410
JHOH495
JHOH496
JHOH498
JHOH499
JHOH500
JHOH501
KHOH484
KHOH485

site_idEC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI J 403
ChainResidue
JPRO97
JPHE98
JILE122
JASN146
JARG284
JHIS332
JNAD401

site_idEC8
Number of Residues33
DetailsBINDING SITE FOR RESIDUE NAD K 401
ChainResidue
KILE122
KASN146
KVAL147
KVAL150
KGLY200
KARG201
KILE202
KASP221
KARG222
KMET255
KPRO256
KASN282
KALA283
KARG284
KASP308
KVAL309
KHIS332
KSER334
KGLY335
KGLN376
KAZI403
KHOH509
KHOH510
KHOH512
KHOH513
KHOH514
KHOH515
KHOH516
KHOH517
KHOH519
KHOH520
KHOH521
KHOH645

site_idEC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI K 403
ChainResidue
KPRO97
KPHE98
KILE122
KASN146
KARG284
KHIS332
KNAD401

site_idFC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 K 8
ChainResidue
IHOH633
KGOL14
KLYS115
KTHR138
KLYS369
KHOH524

site_idFC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE GOL K 14
ChainResidue
KSO48
KARG354
KTYR355
KGLY358
KGLU359
KPHE361
KTYR366
KHOH629
KHOH630

site_idFC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL K 15
ChainResidue
JGLU364
JHOH405
KTYR366
KLYS369
KGLU372
KALA374
KARG378

site_idFC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE GOL K 24
ChainResidue
KTYR102
KHIS126
KASP128
KHOH522
KHOH624

site_idFC5
Number of Residues34
DetailsBINDING SITE FOR RESIDUE NAD L 401
ChainResidue
LILE122
LASN146
LVAL147
LVAL150
LGLY200
LARG201
LILE202
LASP221
LARG222
LMET255
LPRO256
LASN282
LALA283
LARG284
LASP308
LVAL309
LHIS332
LSER334
LGLY335
LGLN376
LAZI403
LHOH547
LHOH548
LHOH550
LHOH551
LHOH552
LHOH553
LHOH554
LHOH555
LHOH557
LHOH558
LHOH559
LHOH610
LHOH615

site_idFC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE AZI L 403
ChainResidue
LPRO97
LPHE98
LILE122
LASN146
LARG284
LHIS332
LNAD401

site_idFC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL L 21
ChainResidue
LTYR102
LHIS126
LASP128
LHOH388
LHOH560
LHOH644

Functional Information from PROSITE/UniProt
site_idPS00065
Number of Residues28
DetailsD_2_HYDROXYACID_DH_1 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. IGTVGaGRIGklllqrlkpfgcn.LLyHD
ChainResidueDetails
AILE194-ASP221

site_idPS00670
Number of Residues23
DetailsD_2_HYDROXYACID_DH_2 D-isomer specific 2-hydroxyacid dehydrogenases signature 2. MLpkCDVIvINmPltekTrgMfN
ChainResidueDetails
AMET244-ASN266

site_idPS00671
Number of Residues17
DetailsD_2_HYDROXYACID_DH_3 D-isomer specific 2-hydroxyacid dehydrogenases signature 3. LKkGvLIVNnARGaIME
ChainResidueDetails
ALEU273-GLU289

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues24
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_03210
ChainResidueDetails
AILE122
EASN146
FILE122
FASN146
GILE122
GASN146
HILE122
HASN146
IILE122
IASN146
JILE122
AASN146
JASN146
KILE122
KASN146
LILE122
LASN146
BILE122
BASN146
CILE122
CASN146
DILE122
DASN146
EILE122

site_idSWS_FT_FI2
Number of Residues72
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_03210, ECO:0000269|Ref.10
ChainResidueDetails
AARG201
BASN282
BASP308
BHIS332
CARG201
CASP221
CPRO256
CASN282
CASP308
CHIS332
DARG201
AASP221
DASP221
DPRO256
DASN282
DASP308
DHIS332
EARG201
EASP221
EPRO256
EASN282
EASP308
APRO256
EHIS332
FARG201
FASP221
FPRO256
FASN282
FASP308
FHIS332
GARG201
GASP221
GPRO256
AASN282
GASN282
GASP308
GHIS332
HARG201
HASP221
HPRO256
HASN282
HASP308
HHIS332
IARG201
AASP308
IASP221
IPRO256
IASN282
IASP308
IHIS332
JARG201
JASP221
JPRO256
JASN282
JASP308
AHIS332
JHIS332
KARG201
KASP221
KPRO256
KASN282
KASP308
KHIS332
LARG201
LASP221
LPRO256
BARG201
LASN282
LASP308
LHIS332
BASP221
BPRO256

site_idSWS_FT_FI3
Number of Residues24
DetailsSITE: Important for catalytic activity => ECO:0000255|HAMAP-Rule:MF_03210
ChainResidueDetails
AARG284
EHIS332
FARG284
FHIS332
GARG284
GHIS332
HARG284
HHIS332
IARG284
IHIS332
JARG284
AHIS332
JHIS332
KARG284
KHIS332
LARG284
LHIS332
BARG284
BHIS332
CARG284
CHIS332
DARG284
DHIS332
EARG284

219140

PDB entries from 2024-05-01

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