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5C3Y

Structure of human ribokinase crystallized with AMPPNP

Functional Information from GO Data
ChainGOidnamespacecontents
A0004747molecular_functionribokinase activity
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006014biological_processD-ribose metabolic process
A0006098biological_processpentose-phosphate shunt
A0006753biological_processnucleoside phosphate metabolic process
A0016301molecular_functionkinase activity
A0019303biological_processD-ribose catabolic process
A0042802molecular_functionidentical protein binding
A0046835biological_processcarbohydrate phosphorylation
A0046872molecular_functionmetal ion binding
B0004747molecular_functionribokinase activity
B0005515molecular_functionprotein binding
B0005524molecular_functionATP binding
B0005634cellular_componentnucleus
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006014biological_processD-ribose metabolic process
B0006098biological_processpentose-phosphate shunt
B0006753biological_processnucleoside phosphate metabolic process
B0016301molecular_functionkinase activity
B0019303biological_processD-ribose catabolic process
B0042802molecular_functionidentical protein binding
B0046835biological_processcarbohydrate phosphorylation
B0046872molecular_functionmetal ion binding
C0004747molecular_functionribokinase activity
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005634cellular_componentnucleus
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006014biological_processD-ribose metabolic process
C0006098biological_processpentose-phosphate shunt
C0006753biological_processnucleoside phosphate metabolic process
C0016301molecular_functionkinase activity
C0019303biological_processD-ribose catabolic process
C0042802molecular_functionidentical protein binding
C0046835biological_processcarbohydrate phosphorylation
C0046872molecular_functionmetal ion binding
D0004747molecular_functionribokinase activity
D0005515molecular_functionprotein binding
D0005524molecular_functionATP binding
D0005634cellular_componentnucleus
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006014biological_processD-ribose metabolic process
D0006098biological_processpentose-phosphate shunt
D0006753biological_processnucleoside phosphate metabolic process
D0016301molecular_functionkinase activity
D0019303biological_processD-ribose catabolic process
D0042802molecular_functionidentical protein binding
D0046835biological_processcarbohydrate phosphorylation
D0046872molecular_functionmetal ion binding
E0004747molecular_functionribokinase activity
E0005515molecular_functionprotein binding
E0005524molecular_functionATP binding
E0005634cellular_componentnucleus
E0005737cellular_componentcytoplasm
E0005829cellular_componentcytosol
E0006014biological_processD-ribose metabolic process
E0006098biological_processpentose-phosphate shunt
E0006753biological_processnucleoside phosphate metabolic process
E0016301molecular_functionkinase activity
E0019303biological_processD-ribose catabolic process
E0042802molecular_functionidentical protein binding
E0046835biological_processcarbohydrate phosphorylation
E0046872molecular_functionmetal ion binding
F0004747molecular_functionribokinase activity
F0005515molecular_functionprotein binding
F0005524molecular_functionATP binding
F0005634cellular_componentnucleus
F0005737cellular_componentcytoplasm
F0005829cellular_componentcytosol
F0006014biological_processD-ribose metabolic process
F0006098biological_processpentose-phosphate shunt
F0006753biological_processnucleoside phosphate metabolic process
F0016301molecular_functionkinase activity
F0019303biological_processD-ribose catabolic process
F0042802molecular_functionidentical protein binding
F0046835biological_processcarbohydrate phosphorylation
F0046872molecular_functionmetal ion binding
G0004747molecular_functionribokinase activity
G0005515molecular_functionprotein binding
G0005524molecular_functionATP binding
G0005634cellular_componentnucleus
G0005737cellular_componentcytoplasm
G0005829cellular_componentcytosol
G0006014biological_processD-ribose metabolic process
G0006098biological_processpentose-phosphate shunt
G0006753biological_processnucleoside phosphate metabolic process
G0016301molecular_functionkinase activity
G0019303biological_processD-ribose catabolic process
G0042802molecular_functionidentical protein binding
G0046835biological_processcarbohydrate phosphorylation
G0046872molecular_functionmetal ion binding
H0004747molecular_functionribokinase activity
H0005515molecular_functionprotein binding
H0005524molecular_functionATP binding
H0005634cellular_componentnucleus
H0005737cellular_componentcytoplasm
H0005829cellular_componentcytosol
H0006014biological_processD-ribose metabolic process
H0006098biological_processpentose-phosphate shunt
H0006753biological_processnucleoside phosphate metabolic process
H0016301molecular_functionkinase activity
H0019303biological_processD-ribose catabolic process
H0042802molecular_functionidentical protein binding
H0046835biological_processcarbohydrate phosphorylation
H0046872molecular_functionmetal ion binding
I0004747molecular_functionribokinase activity
I0005515molecular_functionprotein binding
I0005524molecular_functionATP binding
I0005634cellular_componentnucleus
I0005737cellular_componentcytoplasm
I0005829cellular_componentcytosol
I0006014biological_processD-ribose metabolic process
I0006098biological_processpentose-phosphate shunt
I0006753biological_processnucleoside phosphate metabolic process
I0016301molecular_functionkinase activity
I0019303biological_processD-ribose catabolic process
I0042802molecular_functionidentical protein binding
I0046835biological_processcarbohydrate phosphorylation
I0046872molecular_functionmetal ion binding
J0004747molecular_functionribokinase activity
J0005515molecular_functionprotein binding
J0005524molecular_functionATP binding
J0005634cellular_componentnucleus
J0005737cellular_componentcytoplasm
J0005829cellular_componentcytosol
J0006014biological_processD-ribose metabolic process
J0006098biological_processpentose-phosphate shunt
J0006753biological_processnucleoside phosphate metabolic process
J0016301molecular_functionkinase activity
J0019303biological_processD-ribose catabolic process
J0042802molecular_functionidentical protein binding
J0046835biological_processcarbohydrate phosphorylation
J0046872molecular_functionmetal ion binding
K0004747molecular_functionribokinase activity
K0005515molecular_functionprotein binding
K0005524molecular_functionATP binding
K0005634cellular_componentnucleus
K0005737cellular_componentcytoplasm
K0005829cellular_componentcytosol
K0006014biological_processD-ribose metabolic process
K0006098biological_processpentose-phosphate shunt
K0006753biological_processnucleoside phosphate metabolic process
K0016301molecular_functionkinase activity
K0019303biological_processD-ribose catabolic process
K0042802molecular_functionidentical protein binding
K0046835biological_processcarbohydrate phosphorylation
K0046872molecular_functionmetal ion binding
L0004747molecular_functionribokinase activity
L0005515molecular_functionprotein binding
L0005524molecular_functionATP binding
L0005634cellular_componentnucleus
L0005737cellular_componentcytoplasm
L0005829cellular_componentcytosol
L0006014biological_processD-ribose metabolic process
L0006098biological_processpentose-phosphate shunt
L0006753biological_processnucleoside phosphate metabolic process
L0016301molecular_functionkinase activity
L0019303biological_processD-ribose catabolic process
L0042802molecular_functionidentical protein binding
L0046835biological_processcarbohydrate phosphorylation
L0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues12
Detailsbinding site for residue AN2 A 401
ChainResidue
ATHR235
AALA298
AALA299
AHOH519
AGLY237
AGLY240
AVAL259
ATHR264
AGLY266
AALA267
AGLY268
AASN295

site_idAC2
Number of Residues6
Detailsbinding site for residue NA A 402
ChainResidue
AASP263
ASER301
AALA304
ASER310
AHOH507
AHOH526

site_idAC3
Number of Residues5
Detailsbinding site for residue NA A 403
ChainResidue
AHOH505
AHOH512
AHOH519
AHOH535
AHOH536

site_idAC4
Number of Residues13
Detailsbinding site for residue AN2 B 401
ChainResidue
BASN199
BTHR235
BGLY237
BGLY240
BVAL259
BTHR264
BGLY266
BALA267
BGLY268
BASN295
BALA298
BHOH542
BHOH549

site_idAC5
Number of Residues6
Detailsbinding site for residue NA B 402
ChainResidue
BASP263
BSER301
BALA304
BSER310
BHOH510
BHOH529

site_idAC6
Number of Residues6
Detailsbinding site for residue NA B 403
ChainResidue
BHOH504
BHOH511
BHOH519
BHOH542
BHOH571
BHOH574

site_idAC7
Number of Residues16
Detailsbinding site for residue AN2 C 401
ChainResidue
CASN199
CTHR235
CGLY237
CALA238
CGLY240
CVAL259
CTHR264
CGLY266
CALA267
CGLY268
CASN295
CALA298
CALA299
CHOH550
CHOH561
CHOH568

site_idAC8
Number of Residues6
Detailsbinding site for residue NA C 402
ChainResidue
CASP263
CSER301
CALA304
CSER310
CHOH505
CHOH512

site_idAC9
Number of Residues6
Detailsbinding site for residue NA C 403
ChainResidue
CHOH501
CHOH502
CHOH524
CHOH540
CHOH550
CHOH561

site_idAD1
Number of Residues12
Detailsbinding site for residue AN2 D 401
ChainResidue
DTHR235
DGLY237
DGLY240
DVAL259
DTHR264
DALA267
DGLY268
DASN295
DALA298
DALA299
DHOH501
DHOH515

site_idAD2
Number of Residues6
Detailsbinding site for residue NA D 402
ChainResidue
DASP263
DSER301
DALA304
DSER310
DHOH516
DHOH517

site_idAD3
Number of Residues6
Detailsbinding site for residue NA D 403
ChainResidue
DHOH560
DHOH511
DHOH512
DHOH527
DHOH547
DHOH558

site_idAD4
Number of Residues14
Detailsbinding site for residue AN2 E 401
ChainResidue
EASN199
ETHR235
EGLY237
EGLY240
EVAL259
ETHR264
EALA267
EGLY268
EASN295
EALA298
EALA299
EHOH516
EHOH529
EHOH553

site_idAD5
Number of Residues6
Detailsbinding site for residue NA E 402
ChainResidue
EASP263
ESER301
EALA304
ESER310
EHOH517
EHOH519

site_idAD6
Number of Residues6
Detailsbinding site for residue NA E 403
ChainResidue
EHOH531
EHOH534
EHOH542
EHOH553
EHOH560
EHOH577

site_idAD7
Number of Residues14
Detailsbinding site for residue AN2 F 401
ChainResidue
FTHR235
FGLY237
FGLY240
FVAL259
FALA261
FTHR264
FGLY266
FALA267
FGLY268
FASN295
FALA298
FALA299
FVAL302
FHOH523

site_idAD8
Number of Residues6
Detailsbinding site for residue NA F 402
ChainResidue
FASP263
FSER301
FALA304
FSER310
FHOH509
FHOH522

site_idAD9
Number of Residues7
Detailsbinding site for residue NA F 403
ChainResidue
FASN199
FHOH501
FHOH516
FHOH523
FHOH527
FHOH534
FHOH544

site_idAE1
Number of Residues16
Detailsbinding site for residue AN2 G 401
ChainResidue
GTHR235
GGLY237
GALA238
GGLY240
GVAL259
GTHR264
GALA267
GGLY268
GASN295
GALA298
GALA299
GHOH502
GHOH506
GHOH507
GHOH521
GHOH531

site_idAE2
Number of Residues6
Detailsbinding site for residue NA G 402
ChainResidue
GASP263
GSER301
GALA304
GSER310
GHOH517
GHOH535

site_idAE3
Number of Residues6
Detailsbinding site for residue NA G 403
ChainResidue
GHOH506
GHOH523
GHOH525
GHOH526
GHOH555
GHOH578

site_idAE4
Number of Residues13
Detailsbinding site for residue AN2 H 401
ChainResidue
HTHR235
HGLY237
HALA238
HGLY240
HVAL259
HTHR264
HGLY268
HASN295
HALA298
HHOH501
HHOH522
HHOH523
HHOH545

site_idAE5
Number of Residues6
Detailsbinding site for residue NA H 402
ChainResidue
HASP263
HSER301
HALA304
HSER310
HHOH509
HHOH514

site_idAE6
Number of Residues6
Detailsbinding site for residue NA H 403
ChainResidue
HHOH522
HHOH524
HHOH526
HHOH539
HHOH545
HHOH568

site_idAE7
Number of Residues14
Detailsbinding site for residue AN2 I 401
ChainResidue
IASN199
ITHR235
IGLY237
IALA238
IGLY240
IVAL259
ITHR264
IGLY266
IALA267
IGLY268
IASN295
IALA298
IALA299
IHOH538

site_idAE8
Number of Residues6
Detailsbinding site for residue NA I 402
ChainResidue
IASP263
ISER301
IALA304
ISER310
IHOH519
IHOH522

site_idAE9
Number of Residues5
Detailsbinding site for residue NA I 403
ChainResidue
IHOH513
IHOH517
IHOH520
IHOH532
IHOH538

site_idAF1
Number of Residues13
Detailsbinding site for residue AN2 J 401
ChainResidue
JTHR235
JGLY237
JALA238
JGLY240
JVAL259
JTHR264
JALA267
JGLY268
JASN295
JALA298
JALA299
JHOH514
JHOH521

site_idAF2
Number of Residues6
Detailsbinding site for residue NA J 402
ChainResidue
JASP263
JSER301
JALA304
JSER310
JHOH505
JHOH513

site_idAF3
Number of Residues6
Detailsbinding site for residue NA J 403
ChainResidue
JHOH503
JHOH504
JHOH514
JHOH521
JHOH528
JHOH530

site_idAF4
Number of Residues14
Detailsbinding site for residue AN2 K 401
ChainResidue
KASN199
KTHR235
KGLY237
KALA238
KGLY240
KVAL259
KTHR264
KGLY266
KALA267
KGLY268
KASN295
KALA298
KALA299
KHOH541

site_idAF5
Number of Residues6
Detailsbinding site for residue NA K 402
ChainResidue
KASP263
KSER301
KALA304
KSER310
KHOH507
KHOH536

site_idAF6
Number of Residues6
Detailsbinding site for residue NA K 403
ChainResidue
KHOH501
KHOH508
KHOH526
KHOH541
KHOH544
KHOH546

site_idAF7
Number of Residues15
Detailsbinding site for residue AN2 L 401
ChainResidue
LASN199
LTHR235
LGLY237
LGLY240
LVAL259
LTHR264
LALA267
LGLY268
LASN295
LALA298
LALA299
LHOH501
LHOH504
LHOH517
LHOH530

site_idAF8
Number of Residues6
Detailsbinding site for residue NA L 402
ChainResidue
LASP263
LSER301
LALA304
LSER310
LHOH516
LHOH522

site_idAF9
Number of Residues6
Detailsbinding site for residue NA L 403
ChainResidue
LHOH515
LHOH521
LHOH524
LHOH530
LHOH534
LHOH539

Functional Information from PROSITE/UniProt
site_idPS00584
Number of Residues14
DetailsPFKB_KINASES_2 pfkB family of carbohydrate kinases signature 2. DTtGAGDsfvGALA
ChainResidueDetails
AASP263-ALA276

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsACT_SITE: Proton acceptor => ECO:0000250|UniProtKB:P0A9J6, ECO:0000255|HAMAP-Rule:MF_03215
ChainResidueDetails
AASP269
JASP269
KASP269
LASP269
BASP269
CASP269
DASP269
EASP269
FASP269
GASP269
HASP269
IASP269

site_idSWS_FT_FI2
Number of Residues72
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P0A9J6, ECO:0000255|HAMAP-Rule:MF_03215
ChainResidueDetails
AMET25
BTHR265
BASP269
BGLY306
CMET25
CGLY53
CGLU154
CTHR265
CASP269
CGLY306
DMET25
AGLY53
DGLY53
DGLU154
DTHR265
DASP269
DGLY306
EMET25
EGLY53
EGLU154
ETHR265
EASP269
AGLU154
EGLY306
FMET25
FGLY53
FGLU154
FTHR265
FASP269
FGLY306
GMET25
GGLY53
GGLU154
ATHR265
GTHR265
GASP269
GGLY306
HMET25
HGLY53
HGLU154
HTHR265
HASP269
HGLY306
IMET25
AASP269
IGLY53
IGLU154
ITHR265
IASP269
IGLY306
JMET25
JGLY53
JGLU154
JTHR265
JASP269
AGLY306
JGLY306
KMET25
KGLY53
KGLU154
KTHR265
KASP269
KGLY306
LMET25
LGLY53
LGLU154
BMET25
LTHR265
LASP269
LGLY306
BGLY53
BGLU154

site_idSWS_FT_FI3
Number of Residues60
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000269|Ref.7
ChainResidueDetails
AASN199
BASN295
CASN199
CTHR235
CTHR256
CGLY268
CASN295
DASN199
DTHR235
DTHR256
DGLY268
ATHR235
DASN295
EASN199
ETHR235
ETHR256
EGLY268
EASN295
FASN199
FTHR235
FTHR256
FGLY268
ATHR256
FASN295
GASN199
GTHR235
GTHR256
GGLY268
GASN295
HASN199
HTHR235
HTHR256
HGLY268
AGLY268
HASN295
IASN199
ITHR235
ITHR256
IGLY268
IASN295
JASN199
JTHR235
JTHR256
JGLY268
AASN295
JASN295
KASN199
KTHR235
KTHR256
KGLY268
KASN295
LASN199
LTHR235
LTHR256
LGLY268
BASN199
LASN295
BTHR235
BTHR256
BGLY268

site_idSWS_FT_FI4
Number of Residues48
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_03215, ECO:0000305|Ref.7
ChainResidueDetails
AASP263
CSER301
CALA304
CSER310
DASP263
DSER301
DALA304
DSER310
EASP263
ESER301
EALA304
ASER301
ESER310
FASP263
FSER301
FALA304
FSER310
GASP263
GSER301
GALA304
GSER310
HASP263
AALA304
HSER301
HALA304
HSER310
IASP263
ISER301
IALA304
ISER310
JASP263
JSER301
JALA304
ASER310
JSER310
KASP263
KSER301
KALA304
KSER310
LASP263
LSER301
LALA304
LSER310
BASP263
BSER301
BALA304
BSER310
CASP263

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PDB entries from 2024-07-24

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