←Back to structures

VP1_protein

Euk-Vir

Tasmanian_aquabirnavirus

VP1_protein__YP_009177609__Tasmanian_aquabirnavirus__1721090

Identity

Accession:: YP_009177609 ↗
Protein ID:: VP1_protein
Kingdom:: euk

Quality

70.4 mean pLDDT

Taxonomy

Orthornavirae› Birnaviridae› Aquabirnavirus› Tasmanian_aquabirnavirus

TaxID: 1721090

Cluster

View cluster (6 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 112-180

PDB

Domain cluster: rep: RNA-dependent_RNA_polymerase__YP_010086266__Lates_calcarifer_birnavirus__2583366__D125-188

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF04197.18 best	Birna_RdRp_palm	97.4	1.40e-27	100.0%	13.4%

D2 medium residues 181-209_241-256_308-357_397-433_451-514

PDB

Domain cluster: rep: VP1_RNA-dependent_RNA_polymerase__NP_690839__Infectious_bursal_disease_virus__10995__D189-259_308-337_421-491

Pfam (3)

Accession	Name	Score	E-value	Q cov	HMM cov
PF04197.18 best	Birna_RdRp_palm	188.2	4.50e-55	52.0%	22.2%
PF04197.18	Birna_RdRp_palm	77.5	1.50e-21	27.6%	10.2%
PF04197.18	Birna_RdRp_palm	31.0	1.80e-07	15.8%	5.5%

D3 medium residues 257-307_434-450

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF04197.18 best	Birna_RdRp_palm	66.2	3.90e-18	76.5%	10.5%

CATH (14)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3zgxA02	6.10.140.1720	Special › Helix non-globular › Helix Hairpins ›	0.63	44.0	4.03e-01	73.5%	81.3%
3fbzA01	1.20.58.800	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.59	49.0	4.27e-01	91.2%	65.7%
4h63K00	1.10.287.3490	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.59	40.0	3.60e-01	70.6%	71.4%
3vhlA02	1.20.58.740	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › DOCK DHR2 domain, lobe C	0.59	51.0	4.24e-01	97.1%	91.7%
4hojA02	1.20.1050.10	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.58	50.0	4.43e-01	100.0%	92.2%
4i43B02	3.30.43.40	Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 › Pre-mRNA-processing-splicing factor 8, U5-snRNA-binding domain	0.56	49.0	4.10e-01	95.6%	89.5%
3d8lA00	1.10.8.940	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein, phage p2 ORF12	0.56	43.0	3.87e-01	80.9%	61.5%
1jr8A00	1.20.120.310	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain	0.56	48.0	4.20e-01	98.5%	77.1%
3ppuB02	1.20.1050.10	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.55	47.0	4.08e-01	100.0%	82.3%
2p6vA00	1.20.120.1110	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › TAFH/NHR1 domain	0.54	46.0	4.16e-01	95.6%	96.9%
2kxpA01	3.30.1140.60	Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › F-actin capping protein, alpha subunit	0.54	45.0	3.86e-01	91.2%	88.8%
4ks9A01	1.20.140.90	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain	0.53	44.0	3.72e-01	97.1%	80.2%
1a41A02	1.20.120.380	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Type 1-topoisomerase catalytic fragment, domain 2	0.53	45.0	4.10e-01	97.1%	97.9%
1f81A00	1.20.1020.10	Mainly Alpha › Up-down Bundle › CREB-binding Protein; Chain A › TAZ domain	0.51	43.0	3.94e-01	91.2%	95.4%

ECOD (11)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
None	—		0.94	89.0	5.14e-01	100.0%	38.7%
1145898	304.48.2.1 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › 'palm' domain in birnaviruse RNA-dependent RNA polymerase › Birna_RdRp_palm	0.94	89.0	5.12e-01	100.0%	37.8%
3289266	4995.1.1.0 ↗	alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like	0.62	52.0	4.81e-01	91.2%	90.6%
3688567	109.4.1.88 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MUN	0.60	51.0	2.94e-01	94.1%	20.2%
3989810	3291.1.1.5 ↗	alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Relaxase_C	0.59	40.0	3.60e-01	97.1%	50.5%
3638639	1128.1.1.1 ↗	alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR	0.57	42.0	3.71e-01	77.9%	85.0%
3705197	574.1.1.1 ↗	alpha bundles › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp	0.55	41.0	3.54e-01	80.9%	58.2%
3309351	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.54	45.0	3.49e-01	94.1%	41.9%
3700138	574.1.1.1 ↗	alpha bundles › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp	0.53	41.0	4.13e-01	85.3%	87.1%
3850519	109.4.1.172 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MMS19_C	0.53	45.0	2.91e-01	98.5%	22.1%
3274262	101.1.2.460 ↗	alpha arrays › HTH › HTH › winged helix domain › WHD_DDX60	0.50	38.0	3.45e-01	82.4%	74.7%

D4 medium residues 358-396_515-582

PDB

Domain cluster: representative

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF20488.4 best	Birna_VP1_thumb	83.3	2.50e-23	56.1%	35.9%
PF04197.18	Birna_RdRp_palm	46.4	3.90e-12	49.5%	7.2%

CATH (12)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1zuyA00	2.30.30.40	Mainly Beta › Roll › SH3 type barrels. › SH3 Domains	0.53	25.0	3.13e-01	98.1%	75.9%
1yn8A00	2.30.30.40	Mainly Beta › Roll › SH3 type barrels. › SH3 Domains	0.53	24.0	2.99e-01	96.3%	69.5%
1zuuA00	2.30.30.40	Mainly Beta › Roll › SH3 type barrels. › SH3 Domains	0.52	25.0	3.08e-01	96.3%	76.8%
2v1qA00	2.30.30.40	Mainly Beta › Roll › SH3 type barrels. › SH3 Domains	0.52	24.0	3.00e-01	96.3%	71.7%
3i35A00	2.30.30.40	Mainly Beta › Roll › SH3 type barrels. › SH3 Domains	0.51	24.0	2.99e-01	96.3%	73.7%
3m8eA00	1.10.10.10	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	0.51	31.0	3.19e-01	100.0%	63.4%
1tbxB00	1.10.10.10	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	0.51	29.0	3.16e-01	99.1%	64.4%
1eupA00	1.10.630.10	Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450	0.51	41.0	2.88e-01	91.6%	63.8%
6vlfA03	2.30.30.40	Mainly Beta › Roll › SH3 type barrels. › SH3 Domains	0.51	24.0	2.96e-01	96.3%	72.4%
4uhiA01	1.10.630.10	Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450	0.51	41.0	2.85e-01	91.6%	70.3%
6l2cB00	3.40.47.10	Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase	0.50	42.0	2.95e-01	95.3%	84.2%
2e5kA01	2.30.30.40	Mainly Beta › Roll › SH3 type barrels. › SH3 Domains	0.50	24.0	3.01e-01	93.5%	73.4%

ECOD (2)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3625911	4.1.1.1 ↗	beta barrels › SH3 › SH3 › SH3 › SH3_1	0.51	24.0	2.87e-01	96.3%	64.6%
3996571	101.1.2.53 ↗	alpha arrays › HTH › HTH › winged helix domain › Mnd1	0.50	26.0	3.29e-01	89.7%	100.0%

D5 medium residues 583-687

PDB

Domain cluster: rep: VP1_RNA-dependent_RNA_polymerase__NP_690839__Infectious_bursal_disease_virus__10995__D603-698

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF20488.4 best	Birna_VP1_thumb	170.5	3.90e-50	100.0%	63.5%