7VIK | pdb_00007vik

Asymmetric unit of cryoEM structure of bacteriophage lambda capsid at 3.76 Angstrom

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)
N	SCOP2B Superfamily	Head decoration protein D (gpD, major capsid protein D)	8043128	3001943	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Head decoration protein D (gpD, major capsid protein D)	8043128	3001943	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Head decoration protein D (gpD, major capsid protein D)	8043128	3001943	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Head decoration protein D (gpD, major capsid protein D)	8043128	3001943	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Head decoration protein D (gpD, major capsid protein D)	8043128	3001943	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Head decoration protein D (gpD, major capsid protein D)	8043128	3001943	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Head decoration protein D (gpD, major capsid protein D)	8043128	3001943	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Phage coat protein-like	8106222	3001529	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Phage coat protein-like	8106222	3001529	SCOP2B (2022-06-29)
E	SCOP2 Family	Phage major capsid protein E	8106221	4004269	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Phage coat protein-like	8106222	3001529	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Phage coat protein-like	8106222	3001529	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phage coat protein-like	8106222	3001529	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phage coat protein-like	8106222	3001529	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phage coat protein-like	8106222	3001529	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)
N	HDPD	e7vikN1	A: beta barrels	X: beta-clip	H: Head decoration protein D (gpD, major capsid protein D) (From Topology)	T: Head decoration protein D (gpD, major capsid protein D)	F: HDPD	ECOD (1.6)
M	HDPD	e7vikM1	A: beta barrels	X: beta-clip	H: Head decoration protein D (gpD, major capsid protein D) (From Topology)	T: Head decoration protein D (gpD, major capsid protein D)	F: HDPD	ECOD (1.6)
L	HDPD	e7vikL1	A: beta barrels	X: beta-clip	H: Head decoration protein D (gpD, major capsid protein D) (From Topology)	T: Head decoration protein D (gpD, major capsid protein D)	F: HDPD	ECOD (1.6)
K	HDPD	e7vikK1	A: beta barrels	X: beta-clip	H: Head decoration protein D (gpD, major capsid protein D) (From Topology)	T: Head decoration protein D (gpD, major capsid protein D)	F: HDPD	ECOD (1.6)
J	HDPD	e7vikJ1	A: beta barrels	X: beta-clip	H: Head decoration protein D (gpD, major capsid protein D) (From Topology)	T: Head decoration protein D (gpD, major capsid protein D)	F: HDPD	ECOD (1.6)
I	HDPD	e7vikI1	A: beta barrels	X: beta-clip	H: Head decoration protein D (gpD, major capsid protein D) (From Topology)	T: Head decoration protein D (gpD, major capsid protein D)	F: HDPD	ECOD (1.6)
H	HDPD	e7vikH1	A: beta barrels	X: beta-clip	H: Head decoration protein D (gpD, major capsid protein D) (From Topology)	T: Head decoration protein D (gpD, major capsid protein D)	F: HDPD	ECOD (1.6)
G	Phage_cap_E	e7vikG1	A: a+b three layers	X: Thioredoxin-like	H: Major capsid protein gp5 (From Topology)	T: Major capsid protein gp5	F: Phage_cap_E	ECOD (1.6)
F	Phage_cap_E	e7vikF1	A: a+b three layers	X: Thioredoxin-like	H: Major capsid protein gp5 (From Topology)	T: Major capsid protein gp5	F: Phage_cap_E	ECOD (1.6)
E	Phage_cap_E	e7vikE1	A: a+b three layers	X: Thioredoxin-like	H: Major capsid protein gp5 (From Topology)	T: Major capsid protein gp5	F: Phage_cap_E	ECOD (1.6)
D	Phage_cap_E	e7vikD1	A: a+b three layers	X: Thioredoxin-like	H: Major capsid protein gp5 (From Topology)	T: Major capsid protein gp5	F: Phage_cap_E	ECOD (1.6)
C	Phage_cap_E	e7vikC1	A: a+b three layers	X: Thioredoxin-like	H: Major capsid protein gp5 (From Topology)	T: Major capsid protein gp5	F: Phage_cap_E	ECOD (1.6)
B	Phage_cap_E	e7vikB1	A: a+b three layers	X: Thioredoxin-like	H: Major capsid protein gp5 (From Topology)	T: Major capsid protein gp5	F: Phage_cap_E	ECOD (1.6)
A	Phage_cap_E	e7vikA1	A: a+b three layers	X: Thioredoxin-like	H: Major capsid protein gp5 (From Topology)	T: Major capsid protein gp5	F: Phage_cap_E	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N	2.40.300.10	Mainly Beta	Beta Barrel	Virus Head Decoration Protein	Chain: A,	CATH (utative)
M	2.40.300.10	Mainly Beta	Beta Barrel	Virus Head Decoration Protein	Chain: A,	CATH (utative)
L	2.40.300.10	Mainly Beta	Beta Barrel	Virus Head Decoration Protein	Chain: A,	CATH (utative)
K	2.40.300.10	Mainly Beta	Beta Barrel	Virus Head Decoration Protein	Chain: A,	CATH (utative)
J	2.40.300.10	Mainly Beta	Beta Barrel	Virus Head Decoration Protein	Chain: A,	CATH (utative)
I	2.40.300.10	Mainly Beta	Beta Barrel	Virus Head Decoration Protein	Chain: A,	CATH (utative)
H	2.40.300.10	Mainly Beta	Beta Barrel	Virus Head Decoration Protein	Chain: A,	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
H, I, J, K, L H, I, J, K, L, M, N	PF02924	Bacteriophage lambda head decoration protein D (HDPD)	Bacteriophage lambda head decoration protein D		Domain
A, B, C, D, E A, B, C, D, E, F, G	PF03864	Phage major capsid protein E (Phage_cap_E)	Phage major capsid protein E	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H, I, J, K, L H, I, J, K, L, M, N	Capsid decoration protein	-	virion assembly viral process viral life cycle viral genome packaging viral DNA genome packaging	viral capsid virion component viral capsid, decoration host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part
A, B, C, D, E A, B, C, D, E, F, G	Major capsid protein	-	-	viral capsid icosahedral viral capsid T=7 icosahedral viral capsid virion component host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H, I, J, K, L H, I, J, K, L, M, N	IPR004195	Head decoration protein D	Family
H, I, J, K, L H, I, J, K, L, M, N	IPR036630	Head decoration protein D superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR005564	Major capsid protein GpE	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.