←Back to structures

capsid_portal_protein

Euk-Vir

Human_herpesvirus_5

capsid_portal_protein__YP_002608292__Human_herpesvirus_5__10359

Identity

Accession:
YP_002608292 ↗
Protein ID:
capsid_portal_protein
Kingdom:
euk

Quality

73.2 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Cytomegalovirus› Human_betaherpesvirus_5

TaxID: 10359

Cluster

View cluster (76 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 88-237
PDB
Domain cluster: rep: capsid_portal_protein__YP_081550__Human_betaherpesvirus_5__10359__D90-194_601-636
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01763.23 best Herpes_UL6 106.3 2.10e-30 100.0% 28.0%
D2 medium residues 238-280
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4mtnA01 3.30.1480.10 Alpha Beta › 2-Layer Sandwich › N Utilization Substance Protein A; Chain:P; domain 4 › NusA, N-terminal domain 0.70 53.0 4.20e-01 86.0% 54.7%
2iz4A02 2.20.25.590 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.68 48.0 4.83e-01 76.7% 88.1%
4dwsA01 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.67 46.0 3.37e-01 72.1% 43.9%
1wxrA03 3.30.160.280 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.66 47.0 3.94e-01 76.7% 81.6%
3oa5A01 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.65 44.0 3.21e-01 72.1% 39.4%
1xhhA00 2.60.40.1900 Mainly Beta › Sandwich › Immunoglobulin-like › Beta-microseminoprotein (PSP94) domain 0.64 45.0 3.67e-01 79.1% 38.5%
6rwcA02 2.20.25.590 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.63 43.0 4.44e-01 72.1% 84.6%
1goiA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.63 45.0 3.58e-01 76.7% 64.4%
6inxA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.62 44.0 3.88e-01 72.1% 58.5%
3hkoA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.62 45.0 2.94e-01 81.4% 67.3%
4gp3A03 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.62 45.0 3.34e-01 81.4% 53.3%
1yw5A01 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.62 48.0 4.43e-01 95.3% 84.1%
4msxA02 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.61 48.0 2.93e-01 90.7% 17.5%
1owqA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.60 42.0 3.66e-01 72.1% 63.2%
1itxA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.60 43.0 3.67e-01 72.1% 63.0%
3wqbA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.60 47.0 3.30e-01 95.3% 86.7%
1ywyA00 3.40.1170.40 Alpha Beta › 3-Layer(aba) Sandwich › MutS, DNA mismatch repair protein, domain I › Protein of unknown function DUF3203 0.57 44.0 3.83e-01 90.7% 90.5%
2vszB02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 40.0 3.19e-01 88.4% 51.3%
7uqyB01 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.56 39.0 2.59e-01 79.1% 70.6%
2fe0A01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.55 40.0 3.05e-01 79.1% 73.8%
4q1vA01 2.140.10.30 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Dipeptidylpeptidase IV, N-terminal domain 0.55 40.0 2.34e-01 83.7% 15.8%
3qf7A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 39.0 2.47e-01 81.4% 16.0%
2mnjB00 2.60.40.4160 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 41.0 3.31e-01 83.7% 88.6%
2lnjA00 3.40.1000.10 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich 0.54 37.0 2.59e-01 76.7% 81.8%
3m7nA03 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.53 35.0 3.61e-01 83.7% 88.2%
1twfI01 2.20.25.10 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.53 37.0 3.69e-01 81.4% 82.6%
1fsuA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.52 37.0 2.26e-01 81.4% 44.7%
2eczA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.51 35.0 3.13e-01 74.4% 70.0%
5upiA01 2.70.98.30 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Golgi alpha-mannosidase II; domain 4 0.50 36.0 2.59e-01 88.4% 70.7%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3464303 4.25.1.0 ↗ beta barrels › SH3 › Auxin response factor dimerization domain and ancillary domain › Auxin response factor dimerization domain and ancillary domain 0.71 49.0 3.32e-01 72.1% 79.4%
4960549 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.66 49.0 4.74e-01 83.7% 88.0%
4449615 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.65 47.0 3.81e-01 81.4% 42.2%
3927052 319.1.1.3 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › CS 0.63 50.0 3.78e-01 90.7% 52.2%
3627795 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 46.0 3.85e-01 88.4% 48.2%
4406214 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.61 43.0 3.49e-01 79.1% 44.1%
2811276 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.60 46.0 3.27e-01 88.4% 64.5%
3448051 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.60 45.0 2.87e-01 86.0% 26.9%
4379527 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.60 43.0 3.62e-01 81.4% 44.7%
5004274 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.59 44.0 3.81e-01 83.7% 57.3%
3260311 10.1.1.8 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › SPRY 0.59 51.0 2.88e-01 100.0% 53.5%
2077327 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.58 43.0 3.52e-01 86.0% 50.0%
4040812 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.57 42.0 3.40e-01 76.7% 40.4%
997 220.2.1.1 ↗ beta barrels › PH domain-like › PA2021-like › PA2021-like › DUF3203 0.57 44.0 3.83e-01 90.7% 90.5%
3947154 101.1.2.70 ↗ alpha arrays › HTH › HTH › winged helix domain › PqqD 0.55 40.0 3.29e-01 79.1% 41.1%
5044430 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.55 38.0 2.42e-01 76.7% 13.9%
3500033 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.55 38.0 3.77e-01 81.4% 76.0%
3501699 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 37.0 3.19e-01 79.1% 41.2%
3593875 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.54 38.0 3.68e-01 81.4% 72.7%
3189994 375.1.1.19 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › RNA_POL_M_15KD 0.53 39.0 3.22e-01 83.7% 45.6%
3382157 4351.1.1.1 ↗ alpha arrays › ATP12-like › ATP12-like › ATP12-like › ATP12 0.53 41.0 2.64e-01 88.4% 100.0%
3505640 375.1.1.19 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › RNA_POL_M_15KD 0.52 36.0 3.41e-01 81.4% 63.3%
3900256 7515.1.1.2 ↗ a/b three-layered sandwiches › Alkaline phosphatase-like › Alkaline phosphatase-like › Alkaline phosphatase-like › Sulfatase 0.52 36.0 2.24e-01 79.1% 29.3%
3262703 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.51 40.0 3.89e-01 97.7% 82.0%
3671328 221.4.1.0 ↗ a+b two layers › beta-Grasp › Nudix › Nudix 0.51 37.0 3.06e-01 95.3% 58.2%
4881976 4.1.1.3 ↗ beta barrels › SH3 › SH3 › SH3 › KOW 0.50 35.0 3.15e-01 81.4% 47.3%
3482313 10.1.1.10 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › MAM 0.50 39.0 2.66e-01 95.3% 74.8%
3359784 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.50 35.0 3.24e-01 79.1% 52.3%
3208203 375.1.1.19 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › RNA_POL_M_15KD 0.50 35.0 3.38e-01 81.4% 69.1%