3DKQ | pdb_00003dkq

Crystal structure of Putative Oxygenase (YP_001051978.1) from SHEWANELLA BALTICA OS155 at 2.26 A resolution

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Ras	e3dkqC2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Ras	ECOD (v294.1)
C	Exop_C	e3dkqC1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Exop_C	ECOD (v294.1)
B	Ras	e3dkqB2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Ras	ECOD (v294.1)
B	Exop_C	e3dkqB1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: Exop_C	ECOD (v294.1)
A	PKHD_C	e3dkqA2	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: HUP domains	T: HUP domains	F: PKHD_C	ECOD (v294.1)
A		e3dkqA3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
C	4.10.860.20	Few Secondary Structures	Irregular	DNA Excision Repair, Uvrb	Chain A	CATH (4.3.0)
B	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
B	4.10.860.20	Few Secondary Structures	Irregular	DNA Excision Repair, Uvrb	Chain A	CATH (4.3.0)
A	2.60.120.620	Mainly Beta	Sandwich	Jelly Rolls	q2cbj1_9rhob like domain	CATH (4.3.0)
A	4.10.860.20	Few Secondary Structures	Irregular	DNA Excision Repair, Uvrb	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF18331	PKHD-type hydroxylase C-terminal domain (PKHD_C)	PKHD-type hydroxylase C-terminal domain	This is the C-terminal domain found in PKHD-type hydroxylase enzymes. Family members are found mostly in Bacteria and carry the 2OG-Fe(II) oxygenase superfamily Pfam:PF13640.	Domain
A, B, C	PF13640	2OG-Fe(II) oxygenase superfamily (2OG-FeII_Oxy_3)	2OG-Fe(II) oxygenase superfamily	This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	PKHD-type hydroxylase Sbal_3634	organic acid binding binding carbohydrate binding vitamin binding ion binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity organic acid binding binding carbohydrate binding vitamin binding ion binding anion binding monosaccharide binding carboxylic acid binding heterocyclic compound binding L-ascorbic acid binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen 2-oxoglutarate-dependent dioxygenase activity catalytic activity dioxygenase activity cation binding transition metal ion binding iron ion binding metal ion binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR006620	Prolyl 4-hydroxylase, alpha subunit	Domain
A, B, C	IPR023550	PKHD-type hydroxylase	Family
A, B, C	IPR044862	Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain	Domain
A, B, C	IPR005123	Oxoglutarate/iron-dependent dioxygenase domain	Domain
A, B, C	IPR041097	PKHD-type hydroxylase C-terminal domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.