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small_capsid_protein

Euk-Vir

Cercopithecine_alphaherpesvirus_9

small_capsid_protein__NP_077438__Cercopithecine_alphaherpesvirus_9__35246

Identity

Accession:
NP_077438 ↗
Protein ID:
small_capsid_protein
Kingdom:
euk

Quality

54.4 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Varicellovirus› Cercopithecine_alphaherpesvirus_9

TaxID: 35246

Cluster

Singleton — not in a non-trivial cluster

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 high residues 16-74
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04496.18 best Herpes_UL35 40.8 3.40e-10 100.0% 61.5%
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4nswB01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.71 53.0 3.43e-01 79.7% 44.5%
7e1lB01 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.70 52.0 3.59e-01 79.7% 26.2%
6t4hA03 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.67 49.0 3.58e-01 79.7% 33.7%
3lphC00 6.10.140.630 Special › Helix non-globular › Helix Hairpins › 0.66 45.0 4.57e-01 83.1% 72.4%
1ciiA02 3.30.305.10 Alpha Beta › 2-Layer Sandwich › Colicin Ia; domain 2 › Colicin Ia; domain 2 0.65 56.0 4.62e-01 93.2% 62.4%
3terA00 1.10.287.3550 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 50.0 3.92e-01 81.4% 66.4%
4b1bA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.64 48.0 2.85e-01 79.7% 13.5%
3a8tA02 1.10.287.890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Crystal structure of tRNA isopentenylpyrophosphate transferase (bh2366) domain 0.63 46.0 3.76e-01 78.0% 79.3%
6cgaC02 1.20.58.860 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 48.0 4.35e-01 81.4% 67.9%
3uuxB01 6.10.280.220 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 49.0 3.94e-01 84.7% 46.4%
2e5yA02 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.62 43.0 4.84e-01 83.1% 95.6%
1n7hB01 3.90.25.10 Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 0.62 55.0 4.56e-01 98.3% 95.0%
3ic9A02 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.62 45.0 4.30e-01 79.7% 77.1%
6lo8F01 1.10.287.810 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Mitochondrial import inner membrane translocase subunit tim13 like domains 0.62 46.0 4.41e-01 79.7% 71.0%
1x04A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.60 46.0 3.15e-01 83.1% 24.0%
1j1jA02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.60 52.0 4.68e-01 100.0% 87.1%
1b06A01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.60 49.0 4.72e-01 89.8% 79.1%
1ykhA00 6.10.140.200 Special › Helix non-globular › Helix Hairpins › 0.60 47.0 4.00e-01 84.7% 53.7%
7wz5A01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.60 51.0 3.77e-01 94.9% 61.6%
4w4kA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.59 46.0 4.11e-01 83.1% 73.2%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.59 48.0 3.98e-01 89.8% 51.0%
3qdkA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 50.0 3.32e-01 98.3% 64.6%
3whjA00 6.10.140.1710 Special › Helix non-globular › Helix Hairpins › 0.59 52.0 4.24e-01 100.0% 81.1%
7mdhA02 3.90.110.10 Alpha Beta › Alpha-Beta Complex › L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 › Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal 0.59 51.0 3.71e-01 100.0% 85.5%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 53.0 4.49e-01 98.3% 96.7%
1wu3I00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.57 49.0 3.65e-01 100.0% 80.1%
2dr1A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.57 50.0 3.80e-01 96.6% 88.1%
1dtoA01 1.10.287.30 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › E2 (early) protein, N terminal domain, subdomain 1 0.57 50.0 4.17e-01 96.6% 77.5%
1bccH00 1.10.287.20 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Ubiquinol-cytochrome C reductase hinge domain 0.57 37.0 3.62e-01 84.7% 60.6%
2jexA01 1.10.287.30 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › E2 (early) protein, N terminal domain, subdomain 1 0.55 49.0 4.14e-01 98.3% 82.3%
2yy5A02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.54 45.0 3.60e-01 91.5% 71.4%
4ep4A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 41.0 3.08e-01 88.1% 95.8%
2jrmA00 1.10.10.620 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › ribosome modulation factor like domain 0.52 38.0 3.88e-01 98.3% 80.0%
3ipiA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.51 42.0 2.76e-01 93.2% 34.3%
4wz9A02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.51 44.0 2.91e-01 96.6% 63.0%
1hjrA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 41.0 3.09e-01 91.5% 55.7%
1epuA04 3.40.50.1910 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Sec1/Munc18 (SM) protein, domain 2 0.51 40.0 2.93e-01 88.1% 80.5%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3216129 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.77 58.0 4.47e-01 79.7% 87.2%
3288128 1079.1.1.7 ↗ alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › SfLAP 0.72 52.0 3.64e-01 76.3% 95.0%
4534734 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.72 51.0 3.93e-01 81.4% 35.2%
3978828 164.1.1.1 ↗ alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › CM_2 0.68 58.0 4.12e-01 91.5% 66.7%
3792423 4207.1.1.38 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › PF30341 0.68 53.0 4.05e-01 83.1% 40.8%
5029796 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.67 51.0 3.98e-01 81.4% 48.3%
3601239 3860.1.1.0 ↗ alpha bundles › Myosin VI lever arm › Myosin VI lever arm › Myosin VI lever arm 0.67 60.0 4.01e-01 100.0% 28.9%
3175401 109.4.1.356 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans 0.66 57.0 3.48e-01 100.0% 21.4%
4016292 192.2.1.18 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › ING 0.66 51.0 3.91e-01 84.7% 40.7%
4010451 3788.1.1.15 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › PF27202 0.65 49.0 4.48e-01 78.0% 76.0%
3694219 616.1.1.23 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › PF28719 0.65 57.0 4.99e-01 100.0% 85.6%
3945539 4168.1.1.1 ↗ alpha duplicates or obligate multimers › HAMP domain › HAMP domain › HAMP domain › HAMP 0.65 51.0 5.14e-01 100.0% 83.3%
3290515 397.7.1.0 ↗ few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 0.65 49.0 5.08e-01 79.7% 85.5%
5035231 4168.1.1.1 ↗ alpha duplicates or obligate multimers › HAMP domain › HAMP domain › HAMP domain › HAMP 0.64 51.0 5.25e-01 100.0% 90.9%
3962381 150.5.1.50 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › EspA_EspE 0.64 48.0 4.34e-01 81.4% 58.7%
3219263 10.35.1.2 ↗ beta sandwiches › jelly-roll › ER-derived vesicles protein Erv41p lumenal domain › ER-derived vesicles protein Erv41p lumenal domain › COPIIcoated_ERV 0.64 49.0 3.10e-01 79.7% 24.3%
4014485 5044.1.1.0 ↗ extended segments › PsbZ-like › PsbZ-like › PsbZ-like 0.64 49.0 4.14e-01 86.4% 50.5%
3642338 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.63 48.0 4.42e-01 81.4% 64.0%
5018716 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.62 47.0 4.42e-01 81.4% 67.1%
3693675 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 48.0 3.60e-01 81.4% 62.2%
4876530 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.62 49.0 4.31e-01 84.7% 65.5%
3230351 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.62 55.0 3.97e-01 100.0% 47.9%
3742018 7094.1.1.2 ↗ alpha bundles › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › LIS_MGM1 0.61 45.0 3.92e-01 98.3% 49.5%
3909150 5063.1.1.15 ↗ alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › OCIA 0.61 46.0 4.19e-01 79.7% 89.3%
3739377 4177.1.1.1 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.61 49.0 3.05e-01 84.7% 23.1%
4879470 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.61 46.0 4.27e-01 81.4% 68.0%
4520394 5063.1.1.1 ↗ alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › PSI_PSAK 0.60 45.0 4.24e-01 78.0% 73.9%
4014996 7094.1.1.0 ↗ alpha bundles › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin 0.60 48.0 4.07e-01 93.2% 52.0%
3919989 192.5.1.19 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › OCIA 0.60 45.0 4.05e-01 79.7% 73.8%
1736237 171.1.1.4 ↗ alpha arrays › RNase III catalytic domain-like › RNase III catalytic domain-like › RNase III catalytic domain-like › Ribonucleas_3_3 0.60 43.0 3.28e-01 76.3% 61.9%
3496839 109.4.1.257 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PDS5 0.59 50.0 2.82e-01 98.3% 14.0%
3578256 5055.1.1.0 ↗ extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel 0.59 43.0 4.17e-01 81.4% 68.6%
2857735 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.59 53.0 4.45e-01 100.0% 80.4%
3514794 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.59 53.0 4.15e-01 100.0% 68.3%
3511834 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.58 47.0 3.84e-01 98.3% 90.8%
3906366 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.58 52.0 3.79e-01 100.0% 49.4%
3441518 3559.1.1.11 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Med28 0.58 45.0 3.54e-01 83.1% 45.0%
5054405 606.1.1.1 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Nop 0.57 49.0 4.16e-01 100.0% 61.0%
None — 0.56 42.0 2.74e-01 81.4% 23.7%
3448960 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.55 45.0 4.09e-01 93.2% 76.5%
3579266 5055.1.1.11 ↗ extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel › Cation_ATPase_N 0.55 41.0 3.85e-01 83.1% 68.0%
5064397 5086.1.1.231 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › Rad50_zn_hook 0.55 46.0 3.16e-01 91.5% 79.5%
5061403 244.3.1.3 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › SufE/NifU › SufE/NifU › CO_deh_flav_C 0.54 43.0 3.52e-01 86.4% 81.8%
3929695 3340.1.1.0 ↗ extended segments › Helical region in REST corepressor 1 › Helical region in REST corepressor 1 › Helical region in REST corepressor 1 0.54 37.0 3.74e-01 71.2% 71.7%
3597412 5076.1.1.0 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier 0.53 47.0 3.05e-01 98.3% 43.0%