Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

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

Chain	GOid	namespace	contents
A	0005506	molecular_function	iron ion binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006449	biological_process	regulation of translational termination
A	0008283	biological_process	cell population proliferation
A	0010494	cellular_component	cytoplasmic stress granule
A	0016491	molecular_function	oxidoreductase activity
A	0016705	molecular_function	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
A	0016706	molecular_function	2-oxoglutarate-dependent dioxygenase activity
A	0018126	biological_process	protein hydroxylation
A	0019511	biological_process	peptidyl-proline hydroxylation
A	0031418	molecular_function	L-ascorbic acid binding
A	0031543	molecular_function	peptidyl-proline dioxygenase activity
A	0031544	molecular_function	peptidyl-proline 3-dioxygenase activity
A	0034063	biological_process	stress granule assembly
A	0046872	molecular_function	metal ion binding
A	0051213	molecular_function	dioxygenase activity
B	0005506	molecular_function	iron ion binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006449	biological_process	regulation of translational termination
B	0008283	biological_process	cell population proliferation
B	0010494	cellular_component	cytoplasmic stress granule
B	0016491	molecular_function	oxidoreductase activity
B	0016705	molecular_function	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
B	0016706	molecular_function	2-oxoglutarate-dependent dioxygenase activity
B	0018126	biological_process	protein hydroxylation
B	0019511	biological_process	peptidyl-proline hydroxylation
B	0031418	molecular_function	L-ascorbic acid binding
B	0031543	molecular_function	peptidyl-proline dioxygenase activity
B	0031544	molecular_function	peptidyl-proline 3-dioxygenase activity
B	0034063	biological_process	stress granule assembly
B	0046872	molecular_function	metal ion binding
B	0051213	molecular_function	dioxygenase activity
C	0005506	molecular_function	iron ion binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006449	biological_process	regulation of translational termination
C	0008283	biological_process	cell population proliferation
C	0010494	cellular_component	cytoplasmic stress granule
C	0016491	molecular_function	oxidoreductase activity
C	0016705	molecular_function	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
C	0016706	molecular_function	2-oxoglutarate-dependent dioxygenase activity
C	0018126	biological_process	protein hydroxylation
C	0019511	biological_process	peptidyl-proline hydroxylation
C	0031418	molecular_function	L-ascorbic acid binding
C	0031543	molecular_function	peptidyl-proline dioxygenase activity
C	0031544	molecular_function	peptidyl-proline 3-dioxygenase activity
C	0034063	biological_process	stress granule assembly
C	0046872	molecular_function	metal ion binding
C	0051213	molecular_function	dioxygenase activity
D	0005506	molecular_function	iron ion binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006449	biological_process	regulation of translational termination
D	0008283	biological_process	cell population proliferation
D	0010494	cellular_component	cytoplasmic stress granule
D	0016491	molecular_function	oxidoreductase activity
D	0016705	molecular_function	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
D	0016706	molecular_function	2-oxoglutarate-dependent dioxygenase activity
D	0018126	biological_process	protein hydroxylation
D	0019511	biological_process	peptidyl-proline hydroxylation
D	0031418	molecular_function	L-ascorbic acid binding
D	0031543	molecular_function	peptidyl-proline dioxygenase activity
D	0031544	molecular_function	peptidyl-proline 3-dioxygenase activity
D	0034063	biological_process	stress granule assembly
D	0046872	molecular_function	metal ion binding
D	0051213	molecular_function	dioxygenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MN A 601

Chain	Residue
A	HIS155
A	ASP157
A	HIS218
A	PD2603
A	HOH715

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL A 602

Chain	Residue
A	HIS155
A	PD2603

site_id	AC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE PD2 A 603

Chain	Residue
A	ASP157
A	TYR169
A	LEU182
A	HIS218
A	VAL220
A	ARG230
A	SER232
A	TRP236
A	MN601
A	GOL602
A	HOH715
A	LEU152
A	HIS155

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN B 601

Chain	Residue
B	HIS155
B	ASP157
B	HIS218
B	PD2603

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL B 602

Chain	Residue
B	HIS155
B	ASP157
B	PD2603

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PD2 B 603

Chain	Residue
B	LEU152
B	HIS155
B	ASP157
B	ILE167
B	TYR169
B	HIS218
B	VAL220
B	ARG230
B	SER232
B	TRP236
B	MN601
B	GOL602

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN C 601

Chain	Residue
C	HIS155
C	ASP157
C	HIS218
C	PD2602

site_id	AC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE PD2 C 602

Chain	Residue
C	LEU152
C	HIS155
C	ASP157
C	ILE167
C	LEU182
C	HIS218
C	VAL220
C	ARG230
C	SER232
C	SER234
C	TRP236
C	MN601

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MN D 601

Chain	Residue
D	HIS155
D	ASP157
D	HIS218
D	PD2603

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL D 602

Chain	Residue
D	LEU152
D	HIS155
D	ARG162
D	PD2603

site_id	BC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE PD2 D 603

Chain	Residue
D	LEU152
D	HIS155
D	ASP157
D	ILE167
D	TYR169
D	LEU182
D	HIS218
D	VAL220
D	ARG230
D	SER232
D	TRP236
D	MN601
D	GOL602

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	420
Details	Domain: {"description":"Fe2OG dioxygenase","evidences":[{"source":"PROSITE-ProRule","id":"PRU00805","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00805","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"25728928","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"25728928","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PROSITE-ProRule","id":"PRU00805","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"25728928","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)