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5CNV

Crystal structure of the dATP inhibited E. coli class Ia ribonucleotide reductase complex bound to GDP and TTP at 3.20 Angstroms resolution

Functional Information from GO Data
ChainGOidnamespacecontents
A0004748molecular_functionribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005829cellular_componentcytosol
A0005971cellular_componentribonucleoside-diphosphate reductase complex
A0006457biological_processprotein folding
A0009185biological_processribonucleoside diphosphate metabolic process
A0009263biological_processdeoxyribonucleotide biosynthetic process
A0009265biological_process2'-deoxyribonucleotide biosynthetic process
A0015949biological_processnucleobase-containing small molecule interconversion
A0016491molecular_functionoxidoreductase activity
A0042802molecular_functionidentical protein binding
A0044183molecular_functionprotein folding chaperone
B0004748molecular_functionribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005829cellular_componentcytosol
B0005971cellular_componentribonucleoside-diphosphate reductase complex
B0006457biological_processprotein folding
B0009185biological_processribonucleoside diphosphate metabolic process
B0009263biological_processdeoxyribonucleotide biosynthetic process
B0009265biological_process2'-deoxyribonucleotide biosynthetic process
B0015949biological_processnucleobase-containing small molecule interconversion
B0016491molecular_functionoxidoreductase activity
B0042802molecular_functionidentical protein binding
B0044183molecular_functionprotein folding chaperone
C0004748molecular_functionribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005829cellular_componentcytosol
C0005971cellular_componentribonucleoside-diphosphate reductase complex
C0006457biological_processprotein folding
C0009185biological_processribonucleoside diphosphate metabolic process
C0009263biological_processdeoxyribonucleotide biosynthetic process
C0009265biological_process2'-deoxyribonucleotide biosynthetic process
C0015949biological_processnucleobase-containing small molecule interconversion
C0016491molecular_functionoxidoreductase activity
C0042802molecular_functionidentical protein binding
C0044183molecular_functionprotein folding chaperone
D0004748molecular_functionribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
D0005515molecular_functionprotein binding
D0005524molecular_functionATP binding
D0005829cellular_componentcytosol
D0005971cellular_componentribonucleoside-diphosphate reductase complex
D0006457biological_processprotein folding
D0009185biological_processribonucleoside diphosphate metabolic process
D0009263biological_processdeoxyribonucleotide biosynthetic process
D0009265biological_process2'-deoxyribonucleotide biosynthetic process
D0015949biological_processnucleobase-containing small molecule interconversion
D0016491molecular_functionoxidoreductase activity
D0042802molecular_functionidentical protein binding
D0044183molecular_functionprotein folding chaperone
E0004748molecular_functionribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
E0005506molecular_functioniron ion binding
E0005515molecular_functionprotein binding
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0005971cellular_componentribonucleoside-diphosphate reductase complex
E0009185biological_processribonucleoside diphosphate metabolic process
E0009263biological_processdeoxyribonucleotide biosynthetic process
E0009265biological_process2'-deoxyribonucleotide biosynthetic process
E0015949biological_processnucleobase-containing small molecule interconversion
E0016491molecular_functionoxidoreductase activity
E0042802molecular_functionidentical protein binding
E0046872molecular_functionmetal ion binding
F0004748molecular_functionribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
F0005506molecular_functioniron ion binding
F0005515molecular_functionprotein binding
F0005737cellular_componentcytoplasm
F0005829cellular_componentcytosol
F0005971cellular_componentribonucleoside-diphosphate reductase complex
F0009185biological_processribonucleoside diphosphate metabolic process
F0009263biological_processdeoxyribonucleotide biosynthetic process
F0009265biological_process2'-deoxyribonucleotide biosynthetic process
F0015949biological_processnucleobase-containing small molecule interconversion
F0016491molecular_functionoxidoreductase activity
F0042802molecular_functionidentical protein binding
F0046872molecular_functionmetal ion binding
G0004748molecular_functionribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
G0005506molecular_functioniron ion binding
G0005515molecular_functionprotein binding
G0005737cellular_componentcytoplasm
G0005829cellular_componentcytosol
G0005971cellular_componentribonucleoside-diphosphate reductase complex
G0009185biological_processribonucleoside diphosphate metabolic process
G0009263biological_processdeoxyribonucleotide biosynthetic process
G0009265biological_process2'-deoxyribonucleotide biosynthetic process
G0015949biological_processnucleobase-containing small molecule interconversion
G0016491molecular_functionoxidoreductase activity
G0042802molecular_functionidentical protein binding
G0046872molecular_functionmetal ion binding
H0004748molecular_functionribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
H0005506molecular_functioniron ion binding
H0005515molecular_functionprotein binding
H0005737cellular_componentcytoplasm
H0005829cellular_componentcytosol
H0005971cellular_componentribonucleoside-diphosphate reductase complex
H0009185biological_processribonucleoside diphosphate metabolic process
H0009263biological_processdeoxyribonucleotide biosynthetic process
H0009265biological_process2'-deoxyribonucleotide biosynthetic process
H0015949biological_processnucleobase-containing small molecule interconversion
H0016491molecular_functionoxidoreductase activity
H0042802molecular_functionidentical protein binding
H0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues18
Detailsbinding site for residue GDP A 801
ChainResidue
ATHR209
ACYS439
AGLU441
ALEU464
AMET620
APRO621
ASER622
AGLU623
ATHR624
ASER625
ASER224
ACYS225
AALA252
AGLY253
AARG298
AGLY299
AASN437
ALEU438

site_idAC2
Number of Residues16
Detailsbinding site for residue DAT A 802
ChainResidue
AVAL7
ALYS9
AARG10
AGLU15
AARG16
AILE17
AASN18
ALYS21
AVAL25
ATHR55
AHIS59
APHE87
ALYS91
AMG803
ATTP804
AHOH901

site_idAC3
Number of Residues3
Detailsbinding site for residue MG A 803
ChainResidue
ADAT802
ATTP804
AHOH901

site_idAC4
Number of Residues10
Detailsbinding site for residue TTP A 804
ChainResidue
ALYS9
ALYS21
AARG24
AVAL25
ATRP28
ALYS91
APHE97
ADAT802
AMG803
AHOH901

site_idAC5
Number of Residues14
Detailsbinding site for residue TTP A 805
ChainResidue
AASP232
ASER233
ALEU234
AARG262
AILE268
AARG269
AHIS275
AMG806
AHOH905
AHOH906
AHOH907
AHOH908
BSER249
BCYS292

site_idAC6
Number of Residues4
Detailsbinding site for residue MG A 806
ChainResidue
ATTP805
AHOH905
AHOH906
AHOH907

site_idAC7
Number of Residues18
Detailsbinding site for residue GDP B 801
ChainResidue
BPRO208
BTHR209
BSER224
BCYS225
BALA252
BGLY253
BARG298
BGLY299
BASN437
BLEU438
BCYS439
BGLU441
BMET620
BPRO621
BSER622
BGLU623
BTHR624
BSER625

site_idAC8
Number of Residues17
Detailsbinding site for residue DAT B 802
ChainResidue
BHOH901
BVAL7
BLYS9
BARG10
BGLU15
BARG16
BILE17
BASN18
BLYS21
BILE22
BVAL25
BTHR55
BHIS59
BPHE87
BLYS91
BMG803
BTTP804

site_idAC9
Number of Residues3
Detailsbinding site for residue MG B 803
ChainResidue
BDAT802
BTTP804
BHOH901

site_idAD1
Number of Residues9
Detailsbinding site for residue TTP B 804
ChainResidue
BLYS9
BLYS21
BARG24
BVAL25
BTRP28
BPHE97
BDAT802
BMG803
BHOH901

site_idAD2
Number of Residues14
Detailsbinding site for residue TTP B 805
ChainResidue
ASER249
ACYS292
BASP232
BSER233
BLEU234
BARG262
BILE268
BARG269
BHIS275
BPHE281
BMG806
BHOH903
BHOH904
BHOH905

site_idAD3
Number of Residues4
Detailsbinding site for residue MG B 806
ChainResidue
BTTP805
BHOH903
BHOH904
BHOH905

site_idAD4
Number of Residues20
Detailsbinding site for residue GDP C 801
ChainResidue
CPRO208
CTHR209
CSER224
CCYS225
CALA252
CGLY253
CARG298
CGLY299
CASN437
CLEU438
CCYS439
CGLU441
CLEU464
CMET620
CPRO621
CSER622
CGLU623
CTHR624
CSER625
CHOH903

site_idAD5
Number of Residues17
Detailsbinding site for residue DAT C 802
ChainResidue
CLYS9
CARG10
CGLU15
CARG16
CILE17
CASN18
CLYS21
CILE22
CVAL25
CTHR55
CHIS59
CILE62
CPHE87
CLYS91
CMG803
CTTP804
CHOH901

site_idAD6
Number of Residues3
Detailsbinding site for residue MG C 803
ChainResidue
CDAT802
CTTP804
CHOH901

site_idAD7
Number of Residues9
Detailsbinding site for residue TTP C 804
ChainResidue
CLYS9
CLYS21
CARG24
CVAL25
CTRP28
CPHE97
CDAT802
CMG803
CHOH901

site_idAD8
Number of Residues13
Detailsbinding site for residue TTP C 805
ChainResidue
CASP232
CSER233
CLEU234
CARG262
CILE268
CARG269
CHIS275
CMG806
CHOH909
CHOH910
CHOH911
DSER249
DCYS292

site_idAD9
Number of Residues4
Detailsbinding site for residue MG C 806
ChainResidue
CTTP805
CHOH909
CHOH910
CHOH911

site_idAE1
Number of Residues19
Detailsbinding site for residue GDP D 801
ChainResidue
DTHR209
DSER224
DCYS225
DALA252
DGLY253
DARG298
DGLY299
DASN437
DLEU438
DCYS439
DGLU441
DLEU464
DMET620
DPRO621
DSER622
DGLU623
DTHR624
DSER625
DHOH904

site_idAE2
Number of Residues16
Detailsbinding site for residue DAT D 802
ChainResidue
DVAL7
DLYS9
DARG10
DGLU15
DARG16
DASN18
DLYS21
DILE22
DVAL25
DTHR55
DHIS59
DPHE87
DLYS91
DMG803
DTTP804
DHOH901

site_idAE3
Number of Residues3
Detailsbinding site for residue MG D 803
ChainResidue
DDAT802
DTTP804
DHOH901

site_idAE4
Number of Residues9
Detailsbinding site for residue TTP D 804
ChainResidue
DLYS9
DLYS21
DARG24
DVAL25
DTRP28
DPHE97
DDAT802
DMG803
DHOH901

site_idAE5
Number of Residues14
Detailsbinding site for residue TTP D 805
ChainResidue
CSER249
CCYS292
DASP232
DSER233
DLEU234
DARG262
DILE268
DARG269
DHIS275
DPHE281
DMG806
DHOH910
DHOH911
DHOH912

site_idAE6
Number of Residues4
Detailsbinding site for residue MG D 806
ChainResidue
DTTP805
DHOH910
DHOH911
DHOH912

site_idAE7
Number of Residues8
Detailsbinding site for residue FEO E 501
ChainResidue
EASP84
EGLU115
EHIS118
EGLU204
EGLU238
EHIS241
EHOH601
EHOH603

site_idAE8
Number of Residues8
Detailsbinding site for residue FEO F 501
ChainResidue
FASP84
FGLU115
FHIS118
FGLU204
FGLU238
FHIS241
FHOH601
FHOH602

site_idAE9
Number of Residues8
Detailsbinding site for residue FEO G 501
ChainResidue
GASP84
GGLU115
GHIS118
GGLU204
GGLU238
GHIS241
GHOH601
GHOH603

site_idAF1
Number of Residues8
Detailsbinding site for residue FEO H 501
ChainResidue
HASP84
HGLU115
HHIS118
HGLU204
HGLU238
HHIS241
HHOH603
HHOH606

Functional Information from PROSITE/UniProt
site_idPS00089
Number of Residues23
DetailsRIBORED_LARGE Ribonucleotide reductase large subunit signature. WeaLresikthGLRNstlSAlmP
ChainResidueDetails
ATRP599-PRO621

site_idPS00368
Number of Residues17
DetailsRIBORED_SMALL Ribonucleotide reductase small subunit signature. SEt.IHSrSYthIirnIV
ChainResidueDetails
ESER114-VAL130

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsACT_SITE:
ChainResidueDetails
ETYR122
FTYR122
GTYR122
HTYR122
CASN437
CGLU441
DASN437
DGLU441

site_idSWS_FT_FI2
Number of Residues24
DetailsBINDING:
ChainResidueDetails
EASP84
FGLU204
FGLU238
FHIS241
GASP84
GGLU115
GHIS118
GGLU204
GGLU238
GHIS241
HASP84
EGLU115
HGLU115
HHIS118
HGLU204
HGLU238
HHIS241
EHIS118
EGLU204
EGLU238
EHIS241
FASP84
FGLU115
FHIS118

site_idSWS_FT_FI3
Number of Residues16
DetailsBINDING: BINDING => ECO:0000269|PubMed:9309223, ECO:0007744|PDB:3R1R
ChainResidueDetails
ALYS9
CGLU15
CTHR55
CLYS91
DLYS9
DGLU15
DTHR55
DLYS91
AGLU15
ATHR55
ALYS91
BLYS9
BGLU15
BTHR55
BLYS91
CLYS9

site_idSWS_FT_FI4
Number of Residues28
DetailsBINDING: BINDING => ECO:0000269|PubMed:9309223, ECO:0007744|PDB:4R1R
ChainResidueDetails
ATHR209
BARG262
BARG269
BASN437
BGLU441
BGLU623
CTHR209
CASP232
CARG262
CARG269
CASN437
AASP232
CGLU441
CGLU623
DTHR209
DASP232
DARG262
DARG269
DASN437
DGLU441
DGLU623
AARG262
AARG269
AASN437
AGLU441
AGLU623
BTHR209
BASP232

site_idSWS_FT_FI5
Number of Residues8
DetailsSITE: Important for hydrogen atom transfer
ChainResidueDetails
ACYS225
ACYS462
BCYS225
BCYS462
CCYS225
CCYS462
DCYS225
DCYS462

site_idSWS_FT_FI6
Number of Residues8
DetailsSITE: Important for electron transfer
ChainResidueDetails
ATYR730
ATYR731
BTYR730
BTYR731
CTYR730
CTYR731
DTYR730
DTYR731

site_idSWS_FT_FI7
Number of Residues8
DetailsSITE: Interacts with thioredoxin/glutaredoxin
ChainResidueDetails
ACYS754
ACYS759
BCYS754
BCYS759
CCYS754
CCYS759
DCYS754
DCYS759

site_idSWS_FT_FI8
Number of Residues4
DetailsMOD_RES: N6-acetyllysine => ECO:0000269|PubMed:18723842
ChainResidueDetails
ALYS283
BLYS283
CLYS283
DLYS283

Catalytic Information from CSA
site_idMCSA1
Number of Residues2
DetailsM-CSA 918
ChainResidueDetails
ETYR122pi-pi interaction, single electron relay
EASP237
ACYS439hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
AGLU441proton acceptor
ACYS462
ATYR730pi-pi interaction, single electron relay
ATYR731pi-pi interaction, single electron relay

site_idMCSA2
Number of Residues2
DetailsM-CSA 918
ChainResidueDetails
FTYR122pi-pi interaction, single electron relay
FASP237
BCYS439hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
BGLU441proton acceptor
BCYS462
BTYR730pi-pi interaction, single electron relay
BTYR731pi-pi interaction, single electron relay

site_idMCSA3
Number of Residues5
DetailsM-CSA 918
ChainResidueDetails
GGLU115
GTYR122pi-pi interaction, single electron relay
GASP237
GGLU350
GTYR356
CTYR730pi-pi interaction, single electron relay
CTYR731pi-pi interaction, single electron relay

site_idMCSA4
Number of Residues2
DetailsM-CSA 918
ChainResidueDetails
HTYR122pi-pi interaction, single electron relay
HASP237
DCYS439hydrogen radical acceptor, hydrogen radical donor, single electron acceptor
DGLU441proton acceptor
DCYS462
DTYR730pi-pi interaction, single electron relay
DTYR731pi-pi interaction, single electron relay

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PDB entries from 2024-07-17

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