3VBA | pdb_00003vba

Crystal structure of methanogen 3-isopropylmalate isomerase small subunit

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3vbab1	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
B	d3vbab2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
C	d3vbac_	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
F	d3vbaf_	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
E	d3vbae_	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
D	d3vbad_	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
A	d3vbaa1	Alpha and beta proteins (a/b)	The 'swivelling' beta/beta/alpha domain	LeuD/IlvD-like	automated matches	automated matches	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)
A	d3vbaa2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Methanocaldococcus jannaschii DSM 2661 ) [TaxId: 243232 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	LeuD/IlvD-like	8066077	3000947	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	LeuD/IlvD-like	8066077	3000947	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	LeuD/IlvD-like	8066077	3000947	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	LeuD/IlvD-like	8066077	3000947	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LeuD/IlvD-like	8066077	3000947	SCOP2B (2022-06-29)
A	SCOP2 Family	LeuD-like	8066076	4003492	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	LeuD/IlvD-like	8066077	3000947	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	ABC_tran	e3vbaB1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
C	ABC_tran	e3vbaC1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
F	ABC_tran	e3vbaF1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
E	ABC_tran	e3vbaE1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
D	ABC_tran	e3vbaD1	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: ABC_tran	ECOD (develop294)
A	Ras	e3vbaA1	A: alpha bundles	X: Globin-like	H: Flavoproteins/Phosphotyrosine protein phosphatases-like	T: (Phosphotyrosine protein) phosphatases II	F: Ras	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase	domain 4	CATH (4.3.0)
C	3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase	domain 4	CATH (4.3.0)
F	3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase	domain 4	CATH (4.3.0)
E	3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase	domain 4	CATH (4.3.0)
D	3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase	domain 4	CATH (4.3.0)
A	3.20.19.10	Alpha Beta	Alpha-Beta Barrel	Aconitase	domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00694	Aconitase C-terminal domain (Aconitase_C)	Aconitase C-terminal domain	Members of this family usually also match to Pfam:PF00330. This domain undergoes conformational change in the enzyme mechanism [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Isopropylmalate/citramalate isomerase small subunit	3-isopropylmalate dehydratase activity hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity maleate hydratase activity (R)-2-methylmalate dehydratase activity	oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process amino acid biosynthetic process biosynthetic process isoleucine biosynthetic process branched-chain amino acid biosynthetic process metabolic process oxoacid metabolic process small molecule biosynthetic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process amino acid biosynthetic process biosynthetic process isoleucine biosynthetic process branched-chain amino acid biosynthetic process metabolic process cellular process small molecule metabolic process branched-chain amino acid metabolic process isoleucine metabolic process alpha-amino acid biosynthetic process pyruvate family amino acid biosynthetic process L-leucine metabolic process L-leucine biosynthetic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process proteinogenic amino acid biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR015928	Aconitase/3-isopropylmalate dehydratase, swivel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000573	Aconitase A/isopropylmalate dehydratase small subunit, swivel domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR033940	3-isopropylmalate dehydratase, swivel domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011827	Hydrolyase LeuD/HacB/DmdB	Family
A, B, C, D, E A, B, C, D, E, F	IPR050075	3-isopropylmalate dehydratase small subunit	Family

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.