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4NHY

Crystal structure of human OGFOD1, 2-oxoglutarate and iron-dependent oxygenase domain containing 1, in complex with pyridine-2,4-dicarboxylic acid (2,4-PDCA)

Functional Information from GO Data
ChainGOidnamespacecontents
A0005506molecular_functioniron ion binding
A0005515molecular_functionprotein binding
A0005634cellular_componentnucleus
A0005654cellular_componentnucleoplasm
A0005737cellular_componentcytoplasm
A0005829cellular_componentcytosol
A0006449biological_processregulation of translational termination
A0008283biological_processcell population proliferation
A0010494cellular_componentcytoplasmic stress granule
A0016705molecular_functionoxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
A0016706molecular_function2-oxoglutarate-dependent dioxygenase activity
A0018126biological_processprotein hydroxylation
A0019511biological_processpeptidyl-proline hydroxylation
A0031418molecular_functionL-ascorbic acid binding
A0031543molecular_functionpeptidyl-proline dioxygenase activity
A0031544molecular_functionpeptidyl-proline 3-dioxygenase activity
A0034063biological_processstress granule assembly
A0046872molecular_functionmetal ion binding
A0051213molecular_functiondioxygenase activity
B0005506molecular_functioniron ion binding
B0005515molecular_functionprotein binding
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005737cellular_componentcytoplasm
B0005829cellular_componentcytosol
B0006449biological_processregulation of translational termination
B0008283biological_processcell population proliferation
B0010494cellular_componentcytoplasmic stress granule
B0016705molecular_functionoxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
B0016706molecular_function2-oxoglutarate-dependent dioxygenase activity
B0018126biological_processprotein hydroxylation
B0019511biological_processpeptidyl-proline hydroxylation
B0031418molecular_functionL-ascorbic acid binding
B0031543molecular_functionpeptidyl-proline dioxygenase activity
B0031544molecular_functionpeptidyl-proline 3-dioxygenase activity
B0034063biological_processstress granule assembly
B0046872molecular_functionmetal ion binding
B0051213molecular_functiondioxygenase activity
C0005506molecular_functioniron ion binding
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005654cellular_componentnucleoplasm
C0005737cellular_componentcytoplasm
C0005829cellular_componentcytosol
C0006449biological_processregulation of translational termination
C0008283biological_processcell population proliferation
C0010494cellular_componentcytoplasmic stress granule
C0016705molecular_functionoxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
C0016706molecular_function2-oxoglutarate-dependent dioxygenase activity
C0018126biological_processprotein hydroxylation
C0019511biological_processpeptidyl-proline hydroxylation
C0031418molecular_functionL-ascorbic acid binding
C0031543molecular_functionpeptidyl-proline dioxygenase activity
C0031544molecular_functionpeptidyl-proline 3-dioxygenase activity
C0034063biological_processstress granule assembly
C0046872molecular_functionmetal ion binding
C0051213molecular_functiondioxygenase activity
D0005506molecular_functioniron ion binding
D0005515molecular_functionprotein binding
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005737cellular_componentcytoplasm
D0005829cellular_componentcytosol
D0006449biological_processregulation of translational termination
D0008283biological_processcell population proliferation
D0010494cellular_componentcytoplasmic stress granule
D0016705molecular_functionoxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
D0016706molecular_function2-oxoglutarate-dependent dioxygenase activity
D0018126biological_processprotein hydroxylation
D0019511biological_processpeptidyl-proline hydroxylation
D0031418molecular_functionL-ascorbic acid binding
D0031543molecular_functionpeptidyl-proline dioxygenase activity
D0031544molecular_functionpeptidyl-proline 3-dioxygenase activity
D0034063biological_processstress granule assembly
D0046872molecular_functionmetal ion binding
D0051213molecular_functiondioxygenase activity
Functional Information from PDB Data
site_idAC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MN A 601
ChainResidue
AHIS155
AASP157
AHIS218
APD2603
AHOH715

site_idAC2
Number of Residues2
DetailsBINDING SITE FOR RESIDUE GOL A 602
ChainResidue
AHIS155
APD2603

site_idAC3
Number of Residues13
DetailsBINDING SITE FOR RESIDUE PD2 A 603
ChainResidue
AASP157
ATYR169
ALEU182
AHIS218
AVAL220
AARG230
ASER232
ATRP236
AMN601
AGOL602
AHOH715
ALEU152
AHIS155

site_idAC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MN B 601
ChainResidue
BHIS155
BASP157
BHIS218
BPD2603

site_idAC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE GOL B 602
ChainResidue
BHIS155
BASP157
BPD2603

site_idAC6
Number of Residues12
DetailsBINDING SITE FOR RESIDUE PD2 B 603
ChainResidue
BLEU152
BHIS155
BASP157
BILE167
BTYR169
BHIS218
BVAL220
BARG230
BSER232
BTRP236
BMN601
BGOL602

site_idAC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MN C 601
ChainResidue
CHIS155
CASP157
CHIS218
CPD2602

site_idAC8
Number of Residues12
DetailsBINDING SITE FOR RESIDUE PD2 C 602
ChainResidue
CLEU152
CHIS155
CASP157
CILE167
CLEU182
CHIS218
CVAL220
CARG230
CSER232
CSER234
CTRP236
CMN601

site_idAC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MN D 601
ChainResidue
DHIS155
DASP157
DHIS218
DPD2603

site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL D 602
ChainResidue
DLEU152
DHIS155
DARG162
DPD2603

site_idBC2
Number of Residues13
DetailsBINDING SITE FOR RESIDUE PD2 D 603
ChainResidue
DLEU152
DHIS155
DASP157
DILE167
DTYR169
DLEU182
DHIS218
DVAL220
DARG230
DSER232
DTRP236
DMN601
DGOL602

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00805, ECO:0000269|PubMed:25728928
ChainResidueDetails
AHIS155
DHIS155
DASP157
DHIS218
AASP157
AHIS218
BHIS155
BASP157
BHIS218
CHIS155
CASP157
CHIS218

site_idSWS_FT_FI2
Number of Residues4
DetailsBINDING: BINDING => ECO:0000305|PubMed:25728928
ChainResidueDetails
ATYR169
BTYR169
CTYR169
DTYR169

site_idSWS_FT_FI3
Number of Residues4
DetailsBINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00805, ECO:0000305|PubMed:25728928
ChainResidueDetails
AARG230
BARG230
CARG230
DARG230

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PDB entries from 2024-07-10

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