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capsid_protein

Euk-Vir

Cricetid_gammaherpesvirus_2

capsid_protein__YP_004207862__Cricetid_gammaherpesvirus_2__1605972

Identity

Accession:
YP_004207862 ↗
Protein ID:
capsid_protein
Kingdom:
euk

Quality

85.0 mean pLDDT

3D Structure

Domains

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

D1 high residues 1-154_295-315
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01802.24 best Herpes_V23 152.6 2.10e-44 80.0% 45.3%
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2w5eA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.75 24.0 3.70e-01 91.4% 67.6%
6oqrA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.63 23.0 3.23e-01 77.7% 65.6%
1vhkA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.61 24.0 3.65e-01 76.6% 86.3%
1nxzA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.60 23.0 3.56e-01 76.0% 84.7%
3gg8C03 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.58 26.0 3.47e-01 78.3% 76.3%
2xzlA02 2.40.30.230 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.58 24.0 3.58e-01 80.0% 87.3%
8eq1A01 2.40.33.10 Mainly Beta › Beta Barrel › M1 Pyruvate Kinase; Domain 3 › PK beta-barrel domain-like 0.57 26.0 3.55e-01 76.6% 84.1%
2egvA01 2.40.240.20 Mainly Beta › Beta Barrel › Ribosomal Protein L25; Chain P › Hypothetical PUA domain-like; domain 1 0.53 21.0 3.12e-01 81.7% 86.4%
3zn6A02 2.60.40.3410 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 24.0 3.38e-01 73.1% 86.2%
3w1eA03 2.40.10.410 Mainly Beta › Beta Barrel › Thrombin, subunit H › FlgT, C-terminal domain 0.52 25.0 3.51e-01 78.9% 92.1%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5076995 1.1.7.17 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.62 25.0 3.72e-01 78.9% 82.5%
4049740 1.1.9.20 beta barrels › cradle loop barrel › RIFT-related › PUA domain › PUA_4 0.62 24.0 3.65e-01 76.6% 84.0%
5020710 1.1.9.23 beta barrels › cradle loop barrel › RIFT-related › PUA domain › DUF473 0.59 32.0 3.90e-01 90.9% 81.7%
4337888 1.1.15.1 beta barrels › cradle loop barrel › RIFT-related › PK beta-barrel domain-like › PK 0.59 26.0 3.38e-01 78.3% 72.0%
3452625 1.1.7.69 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › MOV-10_beta-barrel 0.58 26.0 3.40e-01 77.7% 73.0%
4085589 1.1.7.17 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.57 24.0 3.62e-01 78.3% 88.7%
4350337 1.1.7.17 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.57 20.0 2.95e-01 78.9% 68.0%
4429352 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.57 26.0 3.60e-01 89.7% 84.4%
3481480 1.1.15.1 beta barrels › cradle loop barrel › RIFT-related › PK beta-barrel domain-like › PK 0.57 27.0 3.59e-01 76.6% 81.0%
3893654 1.1.7.69 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › MOV-10_beta-barrel 0.56 27.0 3.34e-01 80.0% 70.4%
3517355 1.1.8.20 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › Beta-barrel_CAF17_C 0.56 27.0 3.64e-01 79.4% 87.8%
3397088 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.55 32.0 3.96e-01 77.7% 87.8%
4468653 1.1.15.1 beta barrels › cradle loop barrel › RIFT-related › PK beta-barrel domain-like › PK 0.54 25.0 3.45e-01 74.3% 83.2%
4984743 1.1.15.1 beta barrels › cradle loop barrel › RIFT-related › PK beta-barrel domain-like › PK 0.53 26.0 3.47e-01 74.3% 85.3%
3829837 1.1.15.0 beta barrels › cradle loop barrel › RIFT-related › PK beta-barrel domain-like 0.52 28.0 3.40e-01 96.0% 79.1%
5069810 1.1.8.4 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › eIF2_C 0.52 24.0 3.46e-01 74.9% 95.0%
4143576 1.1.9.20 beta barrels › cradle loop barrel › RIFT-related › PUA domain › PUA_4 0.52 21.0 3.13e-01 76.0% 88.6%
4883589 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.51 25.0 3.37e-01 91.4% 86.5%
D2 medium residues 155-218
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01802.24 best Herpes_V23 40.7 2.60e-10 100.0% 19.9%
D3 medium residues 219-292
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01802.24 best Herpes_V23 55.0 1.10e-14 100.0% 26.7%
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5cwkA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.81 46.0 3.42e-01 100.0% 25.0%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.73 46.0 3.99e-01 100.0% 43.6%
2oznB01 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.72 43.0 4.18e-01 100.0% 55.0%
4nsmA00 6.10.250.2770 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.72 45.0 4.58e-01 100.0% 66.2%
3t98B00 6.10.140.1350 Special › Helix non-globular › Helix Hairpins › 0.71 47.0 4.52e-01 100.0% 59.3%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 43.0 4.36e-01 100.0% 63.5%
3eabE00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.68 45.0 4.33e-01 100.0% 59.3%
1w9rA00 1.20.58.440 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › choline binding protein A 0.67 42.0 3.59e-01 100.0% 39.5%
2xubA05 6.10.140.1450 Special › Helix non-globular › Helix Hairpins › 0.65 45.0 4.10e-01 100.0% 55.2%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.63 38.0 3.87e-01 100.0% 60.0%
4mtxD00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.63 45.0 4.14e-01 100.0% 58.9%
3terA00 1.10.287.3550 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 42.0 3.59e-01 100.0% 43.7%
3lnnB03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.63 40.0 4.17e-01 100.0% 71.6%
2m6uA00 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.62 33.0 3.19e-01 82.4% 46.3%
1u00A02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.62 39.0 3.64e-01 95.9% 50.0%
2jbwA01 1.20.1440.110 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › acylaminoacyl peptidase 0.61 38.0 3.43e-01 100.0% 44.7%
2mtqA00 1.20.58.130 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 37.0 3.75e-01 98.6% 60.3%
2btqB03 1.10.287.600 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.61 42.0 4.87e-01 95.9% 100.0%
1gaxA05 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.61 48.0 4.84e-01 100.0% 83.6%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.60 39.0 3.89e-01 100.0% 65.3%
2gtaA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.59 35.0 3.20e-01 71.6% 45.4%
2ckzA01 6.10.140.870 Special › Helix non-globular › Helix Hairpins › 0.58 36.0 4.11e-01 98.6% 95.8%
3bjdA01 1.10.1240.20 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Lytic transglycosylase, superhelical linker domain 0.56 36.0 3.40e-01 100.0% 53.4%
3e22A03 1.10.287.600 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.56 36.0 4.04e-01 100.0% 90.7%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.54 47.0 4.20e-01 100.0% 67.0%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.54 45.0 4.39e-01 100.0% 81.5%
1kblA05 1.20.80.30 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.53 33.0 3.15e-01 94.6% 52.8%
2dq0A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.53 48.0 4.16e-01 100.0% 66.4%
4m52A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 38.0 2.76e-01 75.7% 90.1%
2rd0B00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 44.0 3.56e-01 100.0% 48.2%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.53 48.0 4.11e-01 100.0% 64.3%
1t72A02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.53 45.0 4.08e-01 100.0% 69.4%
1jmuB03 1.10.2050.10 Mainly Alpha › Orthogonal Bundle › Protein mu-1, chain B, domain 3 › Protein mu-1, chain B, domain 3 0.53 37.0 2.89e-01 89.2% 34.4%
3h3mA00 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.52 39.0 3.67e-01 100.0% 66.3%
2fb5A01 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.51 42.0 4.25e-01 100.0% 91.7%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.51 46.0 4.57e-01 100.0% 94.8%
1h7cA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 46.0 4.11e-01 100.0% 71.8%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.50 46.0 4.14e-01 100.0% 72.5%
4u7iA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.50 37.0 3.53e-01 100.0% 64.5%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4149566 3922.1.1.0 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.79 43.0 2.92e-01 100.0% 16.0%
3528259 3922.1.1.0 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.74 47.0 4.90e-01 100.0% 69.6%
3936036 375.10.1.1 few secondary structure elements › Rubredoxin-like › Zinc finger domain of DNA polymerase-alpha › Zinc finger domain of DNA polymerase-alpha › zf-DNA_Pol 0.68 51.0 4.34e-01 100.0% 50.4%
3832267 192.5.1.0 alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.67 48.0 4.31e-01 100.0% 55.0%
4673 192.7.1.4 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.60 47.0 5.02e-01 100.0% 92.4%
3561223 5021.1.1.0 extended segments › Subunit IX of photosystem I reaction centre, PsaJ › Subunit IX of photosystem I reaction centre, PsaJ › Subunit IX of photosystem I reaction centre, PsaJ 0.60 43.0 4.17e-01 100.0% 68.8%
3635376 3755.3.1.298 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › ING 0.59 48.0 3.81e-01 100.0% 46.7%
3575083 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.58 40.0 3.68e-01 100.0% 54.0%
320075 632.6.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit › Epsilon_antitox 0.58 39.0 3.59e-01 100.0% 53.7%
3414133 3324.1.1.2 extended segments › Helical arch in Ski2-like helicases › Helical arch in Ski2-like helicases › Helical arch in Ski2-like helicases 0.57 45.0 3.82e-01 86.5% 79.2%
4937093 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.57 43.0 3.71e-01 100.0% 50.8%
4975359 4995.1.1.0 alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like 0.57 39.0 3.79e-01 100.0% 63.5%
4045132 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.56 48.0 4.18e-01 100.0% 61.8%
3436766 611.9.1.4 alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain › Rx_N 0.56 37.0 3.18e-01 100.0% 40.8%
4016111 604.9.1.0 alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 0.56 35.0 3.55e-01 100.0% 62.7%
3516337 604.7.1.0 alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A 0.55 41.0 3.61e-01 100.0% 53.6%
3931859 4106.1.1.1 few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.55 39.0 2.83e-01 77.0% 74.6%
3171466 3755.3.1.459 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › AIM11_N 0.53 46.0 3.98e-01 100.0% 62.7%
4984763 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.53 38.0 2.73e-01 100.0% 27.3%
3757027 150.1.1.119 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Clusterin 0.52 48.0 3.63e-01 100.0% 48.5%
3799245 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.51 43.0 2.89e-01 100.0% 89.3%
5040013 604.3.1.0 alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.51 40.0 3.82e-01 100.0% 71.1%
3971224 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.51 45.0 3.12e-01 98.6% 31.1%
3500905 604.13.1.1 alpha bundles › Spectrin repeat-like › USP8 N-terminal domain-like › USP8 N-terminal domain-like › USP8_dimer 0.50 46.0 3.82e-01 100.0% 87.2%
3601984 601.1.1.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.50 43.0 3.73e-01 97.3% 83.3%