2QMI

Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family 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)
A	Pab87_oct	e2qmiA3	A: beta barrels	X: Lipocalins/Streptavidin	H: D-aminopeptidase, middle and C-terminal domains (From Topology)	T: D-aminopeptidase, middle and C-terminal domains	F: Pab87_oct	ECOD (1.6)
A	Beta-lactamase_1st	e2qmiA1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
A	Beta-lactamase_2nd	e2qmiA2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)
B	Pab87_oct	e2qmiB3	A: beta barrels	X: Lipocalins/Streptavidin	H: D-aminopeptidase, middle and C-terminal domains (From Topology)	T: D-aminopeptidase, middle and C-terminal domains	F: Pab87_oct	ECOD (1.6)
B	Beta-lactamase_1st	e2qmiB1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
B	Beta-lactamase_2nd	e2qmiB2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)
C	Pab87_oct	e2qmiC3	A: beta barrels	X: Lipocalins/Streptavidin	H: D-aminopeptidase, middle and C-terminal domains (From Topology)	T: D-aminopeptidase, middle and C-terminal domains	F: Pab87_oct	ECOD (1.6)
C	Beta-lactamase_1st	e2qmiC1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
C	Beta-lactamase_2nd	e2qmiC2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)
D	Pab87_oct	e2qmiD3	A: beta barrels	X: Lipocalins/Streptavidin	H: D-aminopeptidase, middle and C-terminal domains (From Topology)	T: D-aminopeptidase, middle and C-terminal domains	F: Pab87_oct	ECOD (1.6)
D	Beta-lactamase_1st	e2qmiD1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
D	Beta-lactamase_2nd	e2qmiD2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)
E	Pab87_oct	e2qmiE3	A: beta barrels	X: Lipocalins/Streptavidin	H: D-aminopeptidase, middle and C-terminal domains (From Topology)	T: D-aminopeptidase, middle and C-terminal domains	F: Pab87_oct	ECOD (1.6)
E	Beta-lactamase_1st	e2qmiE1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
E	Beta-lactamase_2nd	e2qmiE2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)
F	Pab87_oct	e2qmiF3	A: beta barrels	X: Lipocalins/Streptavidin	H: D-aminopeptidase, middle and C-terminal domains (From Topology)	T: D-aminopeptidase, middle and C-terminal domains	F: Pab87_oct	ECOD (1.6)
F	Beta-lactamase_1st	e2qmiF1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
F	Beta-lactamase_2nd	e2qmiF2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)
G	Pab87_oct	e2qmiG3	A: beta barrels	X: Lipocalins/Streptavidin	H: D-aminopeptidase, middle and C-terminal domains (From Topology)	T: D-aminopeptidase, middle and C-terminal domains	F: Pab87_oct	ECOD (1.6)
G	Beta-lactamase_1st	e2qmiG1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
G	Beta-lactamase_2nd	e2qmiG2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)
H	Pab87_oct	e2qmiH3	A: beta barrels	X: Lipocalins/Streptavidin	H: D-aminopeptidase, middle and C-terminal domains (From Topology)	T: D-aminopeptidase, middle and C-terminal domains	F: Pab87_oct	ECOD (1.6)
H	Beta-lactamase_1st	e2qmiH1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_1st	ECOD (1.6)
H	Beta-lactamase_2nd	e2qmiH2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Beta-lactamase_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
A	2.40.128.210	Mainly Beta	Beta Barrel	Lipocalin	Pab87 octamerisation domain	CATH (4.3.0)
B	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
B	2.40.128.210	Mainly Beta	Beta Barrel	Lipocalin	Pab87 octamerisation domain	CATH (4.3.0)
C	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
C	2.40.128.210	Mainly Beta	Beta Barrel	Lipocalin	Pab87 octamerisation domain	CATH (4.3.0)
D	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
D	2.40.128.210	Mainly Beta	Beta Barrel	Lipocalin	Pab87 octamerisation domain	CATH (4.3.0)
E	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
E	2.40.128.210	Mainly Beta	Beta Barrel	Lipocalin	Pab87 octamerisation domain	CATH (4.3.0)
F	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
F	2.40.128.210	Mainly Beta	Beta Barrel	Lipocalin	Pab87 octamerisation domain	CATH (4.3.0)
G	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
G	2.40.128.210	Mainly Beta	Beta Barrel	Lipocalin	Pab87 octamerisation domain	CATH (4.3.0)
H	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
H	2.40.128.210	Mainly Beta	Beta Barrel	Lipocalin	Pab87 octamerisation domain	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	PF13969	Pab87 octamerisation domain (Pab87_oct)	Pab87 octamerisation domain	This domain was first characterised as the C-terminal domain of Pab87 serine protease from Pyrococcus abyssi [1]. The domain is reported to play a crucial role in Pab87 octamerisation and active site compartmentalisation. Its up-and-down 8-stranded b ...	This domain was first characterised as the C-terminal domain of Pab87 serine protease from Pyrococcus abyssi [1]. The domain is reported to play a crucial role in Pab87 octamerisation and active site compartmentalisation. Its up-and-down 8-stranded beta-barrel 3D structure is reminiscent of the one found in lipocalins.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF00144	Beta-lactamase (Beta-lactamase)	Beta-lactamase	This family appears to be distantly related to Pfam:PF00905 and PF00768 D-alanyl-D-alanine carboxypeptidase.	Domain

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001466	Beta-lactamase-related	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR025879	Pab87 octamerisation domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR038164	Pab87 octamerisation domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR050491	Bacterial Cell Wall Synthesis and Modification	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.

Prepare Data

Validate Data

Deposit Data

Help and Resources

2QMI

Structure of the octameric penicillin-binding protein homologue from Pyrococcus abyssi

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage