5IM5 | pdb_00005im5

Crystal structure of designed two-component self-assembling icosahedral cage I53-40

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
AA [auth 1]	SCOP2 Family	Class I aldolase	8069994	4003216	SCOP2 (2022-06-29)
AA [auth 1]	SCOP2 Superfamily	Aldolase	8069995	3000445	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)
O [auth J]	DMRL_synthase	e5im5J1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
N [auth I]	DMRL_synthase	e5im5I1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
M [auth H]	DMRL_synthase	e5im5H1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
L [auth G]	DMRL_synthase	e5im5G1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
K [auth F]	DMRL_synthase	e5im5F1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
J [auth E]	DMRL_synthase	e5im5E1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
I [auth D]	DMRL_synthase	e5im5D1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
H [auth C]	DMRL_synthase	e5im5C1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
G [auth B]	DMRL_synthase	e5im5B1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
F [auth A]	DMRL_synthase	e5im5A1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
E [auth S]	DMRL_synthase	e5im5S1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
D [auth Q]	DMRL_synthase	e5im5Q1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
C [auth O]	DMRL_synthase	e5im5O1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
B [auth M]	DMRL_synthase	e5im5M1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
A [auth K]	DMRL_synthase	e5im5K1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Lumazine synthase	F: DMRL_synthase	ECOD (1.6)
Z [auth 4]	Aldolase	e5im541	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
Y [auth 2]	Aldolase	e5im521	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
X	Aldolase	e5im5X1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
W [auth Z]	Aldolase	e5im5Z1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
V [auth Y]	Aldolase	e5im5Y1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
U	Aldolase	e5im5U1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
T [auth W]	Aldolase	e5im5W1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
S [auth V]	Aldolase	e5im5V1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
R [auth N]	Aldolase	e5im5N1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
Q [auth T]	Aldolase	e5im5T1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
P	Aldolase	e5im5P1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
DA [auth 3]	Aldolase	e5im531	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
CA [auth R]	Aldolase	e5im5R1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
BA [auth L]	Aldolase	e5im5L1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)
AA [auth 1]	Aldolase	e5im511	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Aldolase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
O [auth J]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
N [auth I]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
M [auth H]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
L [auth G]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
K [auth F]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
J [auth E]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
I [auth D]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
H [auth C]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
G [auth B]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
F [auth A]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
E [auth S]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
D [auth Q]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
C [auth O]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
B [auth M]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
A [auth K]	3.40.50.960	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Lumazine/riboflavin synthase	CATH (4.3.0)
Z [auth 4]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
Y [auth 2]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
X	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
W [auth Z]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
V [auth Y]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
U	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
T [auth W]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
S [auth V]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
R [auth N]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
Q [auth T]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
P	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
DA [auth 3]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
CA [auth R]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
BA [auth L]	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
AA [auth 1]	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
A [auth K], B [auth M], C [auth O], D [auth Q], E [auth S], A [auth K], B [auth M], C [auth O], D [auth Q], E [auth S], F [auth A], G [auth B], H [auth C], I [auth D], J [auth E], K [auth F], L [auth G], M [auth H], N [auth I], O [auth J]	PF00885	6,7-dimethyl-8-ribityllumazine synthase (DMRL_synthase)	6,7-dimethyl-8-ribityllumazine synthase	This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function f ...	This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example Swiss:O28856. The family contains a number of different subsets including a family of proteins comprising archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases [1]. It has been established that lumazine synthase catalyses the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric [2]. Brucella, a bacterial genus that causes brucellosis, and other Rhizobiales have an atypical riboflavin metabolic pathway. Brucella spp code for both a type-I and a type-II lumazine synthase, and it has been shown that at least one of these two has to be present in order for Brucella to be viable, showing that in the case of Brucella flavin metabolism is implicated in bacterial virulence [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth K], B [auth M], C [auth O], D [auth Q], E [auth S], A [auth K], B [auth M], C [auth O], D [auth Q], E [auth S], F [auth A], G [auth B], H [auth C], I [auth D], J [auth E], K [auth F], L [auth G], M [auth H], N [auth I], O [auth J]	Designed Riboflavin synthase	riboflavin synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity	water-soluble vitamin biosynthetic process small molecule biosynthetic process flavin-containing compound metabolic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process flavin-containing compound biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process riboflavin metabolic process	protein-containing complex catalytic complex riboflavin synthase complex transferase complex
AA [auth 1], BA [auth L], CA [auth R], DA [auth 3], P, AA [auth 1], BA [auth L], CA [auth R], DA [auth 3], P, Q [auth T], R [auth N], S [auth V], T [auth W], U, V [auth Y], W [auth Z], X, Y [auth 2], Z [auth 4]	Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth K], B [auth M], C [auth O], D [auth Q], E [auth S], A [auth K], B [auth M], C [auth O], D [auth Q], E [auth S], F [auth A], G [auth B], H [auth C], I [auth D], J [auth E], K [auth F], L [auth G], M [auth H], N [auth I], O [auth J]	IPR006399	Riboflavin synthase, archaeal	Family
A [auth K], B [auth M], C [auth O], D [auth Q], E [auth S], A [auth K], B [auth M], C [auth O], D [auth Q], E [auth S], F [auth A], G [auth B], H [auth C], I [auth D], J [auth E], K [auth F], L [auth G], M [auth H], N [auth I], O [auth J]	IPR036467	Lumazine/riboflavin synthase superfamily	Homologous Superfamily
A [auth K], B [auth M], C [auth O], D [auth Q], E [auth S], A [auth K], B [auth M], C [auth O], D [auth Q], E [auth S], F [auth A], G [auth B], H [auth C], I [auth D], J [auth E], K [auth F], L [auth G], M [auth H], N [auth I], O [auth J]	IPR002180	Lumazine/riboflavin synthase	Family