4XKM | pdb_00004xkm

Crystal structure of Xylose Isomerase from an human intestinal tract microbe Bacteroides thetaiotaomicron

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)
H	d4xkmh_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
G	d4xkmg_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
F	d4xkmf_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
E	d4xkme_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
D	d4xkmd_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
C	d4xkmc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
B	d4xkmb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)
A	d4xkma_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Xylose isomerase-like	automated matches	automated matches	(Bacteroides thetaiotaomicron VPI-5482 ) [TaxId: 226186 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Xylose isomerase-like	8078204	3000560	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Xylose isomerase-like	8078204	3000560	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Xylose isomerase-like	8078204	3000560	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Xylose isomerase-like	8078204	3000560	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Xylose isomerase-like	8078204	3000560	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Xylose isomerase-like	8078204	3000560	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Xylose isomerase-like	8078204	3000560	SCOP2B (2022-06-29)
A	SCOP2 Family	Xylose isomerase	8078203	4003301	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Xylose isomerase-like	8078204	3000560	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)
H	PI3_PI4_kinase	e4xkmH1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: PI3_PI4_kinase	ECOD (v294.1)
G	PI3_PI4_kinase	e4xkmG1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: PI3_PI4_kinase	ECOD (v294.1)
F	PI3_PI4_kinase	e4xkmF1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: PI3_PI4_kinase	ECOD (v294.1)
E	PI3_PI4_kinase	e4xkmE1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: PI3_PI4_kinase	ECOD (v294.1)
D	PI3_PI4_kinase	e4xkmD1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: PI3_PI4_kinase	ECOD (v294.1)
C	PI3_PI4_kinase	e4xkmC1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: PI3_PI4_kinase	ECOD (v294.1)
B	PI3_PI4_kinase	e4xkmB1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: PI3_PI4_kinase	ECOD (v294.1)
A	PI3_PI4_kinase	e4xkmA1	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Restriction endonuclease-like	T: Restriction endonuclease-like	F: PI3_PI4_kinase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
G	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
F	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
E	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
D	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
C	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
B	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	CATH (4.3.0)
A	3.20.20.150	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Divalent-metal-dependent TIM barrel enzymes	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, G, H	PF01261	Xylose isomerase-like TIM barrel (AP_endonuc_2)	Xylose isomerase-like TIM barrel	This TIM alpha/beta barrel structure is found in xylose isomerase (Swiss:P19148) and in endonuclease IV (Swiss:P12638, EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the ...	This TIM alpha/beta barrel structure is found in xylose isomerase (Swiss:P19148) and in endonuclease IV (Swiss:P12638, EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae [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, G, H	Xylose isomerase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity xylose isomerase activity catalytic activity	monosaccharide metabolic process carbohydrate metabolic process catabolic process carbohydrate catabolic process primary metabolic process D-xylose metabolic process D-xylose catabolic process small molecule metabolic process metabolic process cellular process monosaccharide catabolic process small molecule catabolic process pentose metabolic process pentose catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013022	Xylose isomerase-like, TIM barrel domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013452	Xylose isomerase, bacterial-type	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036237	Xylose isomerase-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001998	Xylose isomerase	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.