Back to structures

ORF59

Euk-Vir

Human_gammaherpesvirus_8

ORF59__YP_001129416__Human_gammaherpesvirus_8__37296

Identity

Accession:
YP_001129416 ↗
Protein ID:
ORF59
Kingdom:
euk

Quality

73.7 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 3-146
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04929.18 best Herpes_DNAp_acc 199.2 1.60e-58 97.9% 35.0%
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hslX00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.98 89.0 6.74e-01 99.3% 46.3%
2z0lA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.89 85.0 6.43e-01 99.3% 48.7%
1t6lA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.88 71.0 5.76e-01 98.6% 48.6%
1b77A00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.71 54.0 4.59e-01 100.0% 50.0%
4trtA03 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.70 55.0 5.94e-01 100.0% 98.3%
5wceA03 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.69 54.0 5.83e-01 100.0% 98.3%
3t0pA02 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.69 53.0 4.80e-01 100.0% 59.6%
6j8yA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.69 57.0 4.69e-01 100.0% 49.0%
1vpkA03 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.69 54.0 5.82e-01 100.0% 99.2%
4rkiA02 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.68 55.0 5.79e-01 100.0% 94.6%
1u7bA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.68 55.0 4.56e-01 100.0% 49.0%
1jqlA03 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.68 52.0 5.66e-01 100.0% 97.5%
2avtA02 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.68 53.0 4.79e-01 100.0% 59.8%
1sxjH01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.68 53.0 5.65e-01 96.5% 95.2%
3a1jB00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.67 59.0 4.74e-01 98.6% 50.6%
8dqwG01 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.67 61.0 5.74e-01 98.6% 97.7%
5aguA03 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.65 53.0 5.60e-01 100.0% 97.6%
2lgnA00 2.60.40.2850 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 21.0 2.93e-01 97.9% 66.7%
2cuhA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 29.0 3.60e-01 80.6% 92.0%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1178585 227.1.1.13 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Herpes_DNAp_acc 0.98 89.0 9.04e-01 99.3% 94.3%
1082803 227.1.1.13 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Herpes_DNAp_acc 0.89 85.0 8.36e-01 100.0% 95.4%
3932752 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.74 59.0 6.26e-01 99.3% 96.8%
3743202 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.73 57.0 6.22e-01 97.2% 98.3%
3728061 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.73 59.0 6.13e-01 100.0% 92.5%
3624709 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.73 58.0 6.13e-01 99.3% 93.8%
4995744 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.73 56.0 5.97e-01 100.0% 93.5%
3478975 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.72 58.0 6.00e-01 97.2% 90.4%
3230926 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.72 58.0 6.08e-01 100.0% 94.6%
3407531 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.72 57.0 5.90e-01 98.6% 89.6%
4650779 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.71 56.0 5.93e-01 100.0% 95.2%
3478161 227.1.1.12 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.70 58.0 6.04e-01 97.2% 94.1%
4437554 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.70 55.0 5.83e-01 100.0% 94.4%
3873544 227.1.1.12 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.70 59.0 6.07e-01 100.0% 94.8%
3789624 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.70 59.0 6.01e-01 97.9% 92.9%
2096126 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.69 54.0 5.77e-01 100.0% 95.9%
5979 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.69 54.0 5.76e-01 100.0% 95.1%
4542774 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.69 54.0 5.84e-01 100.0% 98.3%
2834340 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.69 58.0 5.92e-01 98.6% 92.8%
3625038 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.69 59.0 6.00e-01 97.9% 93.6%
3022412 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.69 59.0 5.96e-01 100.0% 92.3%
4500973 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.69 54.0 5.79e-01 100.0% 96.7%
4876750 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.69 53.0 5.62e-01 100.0% 92.8%
4336156 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.69 54.0 5.80e-01 98.6% 98.3%
3719938 227.1.1.17 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DUF7881_N 0.69 59.0 6.00e-01 99.3% 95.0%
3251868 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.69 58.0 5.89e-01 98.6% 92.9%
3936914 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.68 57.0 5.95e-01 100.0% 97.7%
4162061 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.68 54.0 5.79e-01 100.0% 97.6%
426904 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.68 52.0 5.60e-01 100.0% 95.1%
4508401 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.68 54.0 5.69e-01 100.0% 96.8%
3788671 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.68 63.0 5.99e-01 99.3% 94.5%
3480669 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.68 58.0 5.90e-01 97.9% 93.7%
3478160 227.1.1.12 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.68 56.0 5.92e-01 100.0% 100.0%
3346536 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.67 57.0 5.71e-01 98.6% 89.7%
4466445 227.1.1.12 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.67 62.0 6.10e-01 100.0% 94.2%
4360456 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.67 54.0 5.61e-01 100.0% 93.8%
3598259 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.67 55.0 5.69e-01 96.5% 94.1%
2325189 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.67 55.0 5.66e-01 100.0% 92.7%
3193266 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.67 58.0 5.82e-01 97.9% 93.1%
3785352 227.1.1.12 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.66 60.0 5.76e-01 98.6% 90.9%
3244230 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.66 59.0 5.84e-01 97.9% 92.0%
4608521 227.1.1.12 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.66 60.0 5.37e-01 98.6% 77.0%
3962048 227.1.1.15 a+b two layers › DNA clamp › DNA clamp › DNA clamp › PF26035 0.66 43.0 4.92e-01 98.6% 93.0%
3596476 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.65 59.0 6.01e-01 100.0% 99.3%
3503503 227.1.1.12 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad9 0.65 57.0 5.79e-01 97.2% 95.2%
3406311 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.65 59.0 5.79e-01 97.9% 91.6%
3507498 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.65 57.0 5.69e-01 97.9% 92.0%
3787933 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.65 58.0 5.64e-01 97.9% 92.5%
3787700 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.65 59.0 5.80e-01 100.0% 100.0%
3256387 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.64 58.0 5.71e-01 98.6% 96.1%
3599554 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.64 57.0 5.64e-01 97.9% 92.7%
4027851 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.64 56.0 5.63e-01 97.9% 94.5%
3810053 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.61 56.0 5.52e-01 100.0% 96.8%
3610047 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.61 56.0 5.43e-01 100.0% 93.8%
1178584 227.1.1.13 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Herpes_DNAp_acc 0.60 55.0 5.50e-01 100.0% 98.6%
2926754 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.56 46.0 4.86e-01 96.5% 100.0%
D2 high residues 161-297
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04929.18 best Herpes_DNAp_acc 193.9 6.50e-57 100.0% 33.8%
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3hslX00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.96 94.0 7.03e-01 100.0% 48.1%
2z0lA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.91 87.0 6.45e-01 100.0% 45.3%
1t6lA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.85 70.0 5.59e-01 100.0% 47.0%
3p91A00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.84 66.0 5.28e-01 100.0% 45.3%
6j8yC00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.79 67.0 5.29e-01 100.0% 47.5%
3t0pA02 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.78 61.0 5.35e-01 100.0% 57.0%
5w7zA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.78 58.0 6.41e-01 97.8% 93.8%
3a1jB00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.78 63.0 4.91e-01 100.0% 42.8%
5wceA03 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.77 61.0 6.47e-01 100.0% 94.1%
1u7bA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.77 63.0 5.05e-01 98.5% 46.6%
6j8yA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.76 63.0 5.03e-01 100.0% 46.3%
1dmlA00 3.70.10.10 Alpha Beta › Box › Proliferating Cell Nuclear Antigen › 0.73 60.0 4.78e-01 100.0% 44.6%
2gu3A01 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.68 26.0 3.68e-01 100.0% 72.3%
3d3rA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.52 25.0 3.11e-01 78.8% 73.5%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1178584 227.1.1.13 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Herpes_DNAp_acc 0.96 94.0 9.16e-01 100.0% 94.5%
1082804 227.1.1.13 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Herpes_DNAp_acc 0.91 87.0 8.46e-01 100.0% 92.5%
3251045 227.1.1.6 a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.82 68.0 6.55e-01 100.0% 77.3%
3997015 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.81 68.0 7.00e-01 100.0% 91.5%
5010672 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.81 65.0 6.91e-01 100.0% 95.8%
3551142 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.80 68.0 6.66e-01 100.0% 83.4%
3624708 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.80 66.0 6.74e-01 100.0% 88.1%
4995028 227.1.1.6 a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.79 65.0 6.83e-01 99.3% 94.4%
4542774 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.79 63.0 6.72e-01 100.0% 95.0%
3738030 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.79 67.0 6.77e-01 100.0% 90.4%
3932751 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.78 65.0 6.71e-01 100.0% 92.3%
4057937 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.78 65.0 6.58e-01 100.0% 88.1%
4650779 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.78 62.0 6.49e-01 100.0% 91.2%
4013292 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.78 67.0 6.80e-01 100.0% 91.9%
2096126 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.77 61.0 6.40e-01 100.0% 91.8%
4025727 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.77 68.0 6.76e-01 100.0% 90.7%
426904 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.77 60.0 6.28e-01 100.0% 90.2%
4500973 227.1.1.8 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta_3 0.77 61.0 6.43e-01 100.0% 92.7%
3407530 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.76 66.0 6.68e-01 100.0% 91.9%
3719897 227.1.1.18 a+b two layers › DNA clamp › DNA clamp › DNA clamp › DUF7881_C 0.76 61.0 6.42e-01 99.3% 92.8%
3782606 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.75 66.0 6.49e-01 100.0% 88.3%
5000467 227.1.1.1 a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_N 0.73 63.0 6.43e-01 99.3% 93.3%
4426056 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.73 65.0 6.25e-01 100.0% 83.9%
3081033 227.1.1.4 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Rad1 0.73 62.0 6.49e-01 90.5% 96.9%
3810053 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.72 68.0 6.47e-01 100.0% 92.9%
3789624 227.1.1.0 a+b two layers › DNA clamp › DNA clamp › DNA clamp 0.71 62.0 6.20e-01 99.3% 90.0%
3507499 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.71 63.0 6.41e-01 100.0% 95.6%
3743106 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.70 65.0 6.43e-01 100.0% 93.8%
3625038 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.70 61.0 6.11e-01 99.3% 90.0%
3596476 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.69 64.0 6.38e-01 100.0% 96.5%
3507498 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.68 61.0 5.97e-01 99.3% 88.7%
3244230 227.1.1.11 a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.65 59.0 5.77e-01 99.3% 89.3%
3739521 511.1.1.0 beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain 0.55 31.0 3.58e-01 100.0% 75.0%
4199940 243.3.1.75 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › DUF6504 0.54 27.0 3.09e-01 100.0% 63.1%
4960618 274.1.1.0 a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.54 33.0 3.44e-01 82.5% 64.6%
5066808 274.1.1.0 a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.54 32.0 3.43e-01 94.9% 65.9%
4030967 274.1.1.0 a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.53 38.0 4.11e-01 89.1% 90.3%
3964304 884.1.1.1 a+b two layers › Hypothetical protein YjiA, C-terminal domain › Hypothetical protein YjiA, C-terminal domain › Hypothetical protein YjiA, C-terminal domain › CobW_C 0.51 25.0 3.01e-01 93.4% 68.2%
1678740 4.1.1.40 beta barrels › SH3 › SH3 › SH3 › FeoA 0.51 26.0 3.24e-01 86.1% 82.1%
3386763 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.50 26.0 3.41e-01 92.0% 98.5%