5E0K | pdb_00005e0k

X-ray crystal structure of tryptophan synthase complex from Pyrococcus furiosus at 2.76 A

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
L	d5e0kl_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	automated matches	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
J	d5e0kj_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	automated matches	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
H	d5e0kh_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	automated matches	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
F	d5e0kf_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	automated matches	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
D	d5e0kd_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	automated matches	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
B	d5e0kb_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	automated matches	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
K	d5e0kk_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Tryptophan biosynthesis enzymes	Trp synthase alpha-subunit	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
I	d5e0ki_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Tryptophan biosynthesis enzymes	Trp synthase alpha-subunit	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
G	d5e0kg_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Tryptophan biosynthesis enzymes	Trp synthase alpha-subunit	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
E	d5e0ke_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Tryptophan biosynthesis enzymes	Trp synthase alpha-subunit	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
C	d5e0kc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Tryptophan biosynthesis enzymes	Trp synthase alpha-subunit	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)
A	d5e0ka_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	Tryptophan biosynthesis enzymes	Trp synthase alpha-subunit	(Pyrococcus furiosus DSM 3638 ) [TaxId: 186497 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8033053	3001427	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8033053	3001427	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8033053	3001427	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8033053	3001427	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8033053	3001427	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8033053	3001427	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043261	3000216	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043261	3000216	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043261	3000216	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043261	3000216	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043261	3000216	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8043261	3000216	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	PALP	e5e0kL2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
J	PALP	e5e0kJ2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
H	PALP	e5e0kH2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
F	PALP	e5e0kF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
D	PALP	e5e0kD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
B	PALP	e5e0kB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PALP	ECOD (1.6)
K	Trp_syntA	e5e0kK1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Trp_syntA	ECOD (1.6)
I	Trp_syntA	e5e0kI1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Trp_syntA	ECOD (1.6)
G	Trp_syntA	e5e0kG1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Trp_syntA	ECOD (1.6)
E	Trp_syntA	e5e0kE1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Trp_syntA	ECOD (1.6)
C	Trp_syntA	e5e0kC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Trp_syntA	ECOD (1.6)
A	Trp_syntA	e5e0kA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Trp_syntA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
J	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
H	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
F	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
K	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
I	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H, J B, D, F, H, J, L	PF00291	Pyridoxal-phosphate dependent enzyme (PALP)	Pyridoxal-phosphate dependent enzyme	-	Family
A, C, E, G, I A, C, E, G, I, K	PF00290	Tryptophan synthase alpha chain (Trp_syntA)	Tryptophan synthase alpha chain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H, J B, D, F, H, J, L	Tryptophan synthase beta chain 1	hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity tryptophan synthase activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm
A, C, E, G, I A, C, E, G, I, K	Tryptophan synthase alpha chain	hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity tryptophan synthase activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L	IPR023026	Tryptophan synthase beta chain/beta chain-like	Family
B, D, F, H, J B, D, F, H, J, L	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR006653	Tryptophan synthase, beta chain, conserved site	Conserved Site
B, D, F, H, J B, D, F, H, J, L	IPR001926	Tryptophan synthase beta chain-like, PALP domain	Domain
B, D, F, H, J B, D, F, H, J, L	IPR006654	Tryptophan synthase, beta chain	Family
A, C, E, G, I A, C, E, G, I, K	IPR002028	Tryptophan synthase, alpha chain	Family
A, C, E, G, I A, C, E, G, I, K	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR018204	Tryptophan synthase, alpha chain, active site	Active Site
A, C, E, G, I A, C, E, G, I, K	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B, D, F, H, J B, D, F, H, J, L	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

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.