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Pol

Euk-Vir

Human_immunodeficiency_virus_1

Pol__NP_789740__Human_immunodeficiency_virus_1__11676

Identity

Accession:
NP_789740 ↗
Protein ID:
Pol
Kingdom:
euk

Quality

76.8 mean pLDDT

Taxonomy

Pararnavirae› Artverviricota› Revtraviricetes› Ortervirales› Retroviridae› Lentivirus› Human_immunodeficiency_virus_1

TaxID: 11676

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 50-146
PDB
Domain cluster: rep: NC_029048.2__YP_009221738.1__PHICD211_20135__00153__D2-127
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00077.26 best RVP 102.5 1.90e-29 96.9% 98.0%
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1a94A00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.97 94.0 9.38e-01 100.0% 99.0%
2fivA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.90 85.0 8.01e-01 100.0% 97.3%
1fmbA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.88 82.0 8.04e-01 100.0% 99.0%
3liyA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.84 79.0 7.37e-01 100.0% 98.3%
3slzA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.84 74.0 7.01e-01 94.8% 81.6%
2vijA01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.82 70.0 6.19e-01 89.7% 96.2%
3s8iA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.82 73.0 6.71e-01 95.9% 81.5%
1j71A01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.81 75.0 6.08e-01 100.0% 90.2%
3sqfA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.81 69.0 7.06e-01 91.8% 100.0%
1yg9A02 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.81 68.0 6.09e-01 89.7% 97.7%
1bxoA01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.80 74.0 6.14e-01 100.0% 91.5%
7tbdB01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.80 73.0 6.07e-01 100.0% 93.3%
1mvpA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.79 75.0 7.08e-01 100.0% 97.3%
5c9dB00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.79 73.0 6.73e-01 100.0% 90.8%
2pmaA01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.77 72.0 6.63e-01 100.0% 97.5%
3aupD01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.76 70.0 5.55e-01 100.0% 89.4%
2jysA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.74 63.0 6.54e-01 93.8% 97.8%
1twfA03 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.58 42.0 4.19e-01 84.5% 73.3%
2k75A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 37.0 3.65e-01 91.8% 68.9%
ECOD (75)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.97 95.0 7.08e-01 100.0% 51.7%
2793644 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.97 94.0 9.36e-01 100.0% 98.0%
1249817 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.97 94.0 9.32e-01 100.0% 98.0%
2 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.90 85.0 7.98e-01 100.0% 97.3%
4 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.88 82.0 8.04e-01 100.0% 99.0%
3970790 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.87 81.0 7.41e-01 100.0% 88.7%
3994789 1.1.1.6 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease 0.86 78.0 6.76e-01 95.9% 74.3%
3932187 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.86 77.0 7.37e-01 94.8% 95.5%
3937611 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.86 77.0 7.33e-01 94.8% 94.5%
3926190 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.86 77.0 6.36e-01 94.8% 68.8%
3935794 1.1.1.6 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease 0.86 77.0 6.64e-01 95.9% 72.4%
4171670 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.86 80.0 7.66e-01 100.0% 94.5%
3370298 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.86 76.0 7.23e-01 93.8% 93.6%
3931384 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.86 77.0 7.32e-01 94.8% 96.4%
3936605 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.85 76.0 7.26e-01 94.8% 90.9%
3868675 1.1.1.6 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease 0.85 76.0 6.23e-01 95.9% 61.2%
3735567 1.1.1.6 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease 0.85 76.0 5.69e-01 95.9% 45.8%
5032197 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.85 73.0 6.97e-01 90.7% 87.3%
3608668 1.1.1.6 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease 0.85 76.0 6.48e-01 95.9% 69.3%
3797665 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.85 76.0 6.53e-01 95.9% 72.4%
3447999 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.85 74.0 6.82e-01 92.8% 84.2%
3506527 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.85 75.0 7.47e-01 94.8% 99.0%
3249073 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.84 75.0 6.93e-01 94.8% 85.0%
3274948 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.84 79.0 6.62e-01 100.0% 71.0%
5031162 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.84 73.0 6.89e-01 92.8% 91.3%
3924552 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.84 76.0 7.05e-01 96.9% 90.0%
5031038 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.84 76.0 6.93e-01 96.9% 92.0%
4494100 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.84 78.0 7.04e-01 100.0% 87.5%
4932925 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.84 71.0 6.60e-01 90.7% 93.3%
411665 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.83 71.0 6.74e-01 94.8% 77.2%
4969327 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.83 74.0 6.47e-01 94.8% 84.3%
3941125 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.83 74.0 6.42e-01 95.9% 75.2%
3931849 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.83 74.0 6.71e-01 94.8% 84.0%
3938624 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.83 73.0 6.91e-01 94.8% 87.0%
3934729 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.83 74.0 6.73e-01 95.9% 80.0%
3505920 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.83 73.0 7.00e-01 94.8% 93.6%
3515226 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.83 73.0 7.12e-01 94.8% 98.1%
4933116 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.83 75.0 7.02e-01 96.9% 88.7%
5030532 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.83 70.0 6.62e-01 90.7% 85.2%
3939691 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.82 69.0 7.04e-01 89.7% 100.0%
3520846 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.82 73.0 7.24e-01 95.9% 100.0%
5032277 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.82 76.0 6.92e-01 100.0% 91.2%
3436417 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.82 73.0 6.59e-01 96.9% 80.8%
3773238 1.1.1.6 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease 0.82 73.0 6.55e-01 95.9% 80.8%
3931768 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.82 73.0 6.69e-01 96.9% 82.4%
3934416 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.82 72.0 6.71e-01 95.9% 91.7%
3421072 1.1.1.30 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › PF30863 0.82 73.0 6.88e-01 96.9% 91.3%
3247514 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.82 72.0 7.04e-01 94.8% 99.0%
3513377 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.82 71.0 6.97e-01 93.8% 95.2%
5030771 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.81 72.0 6.82e-01 95.9% 89.6%
3926561 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.81 72.0 6.67e-01 94.8% 85.0%
5049040 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.81 69.0 6.65e-01 90.7% 92.6%
3484754 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.81 72.0 6.90e-01 95.9% 93.6%
3821648 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.81 72.0 6.56e-01 95.9% 85.6%
3 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.81 76.0 7.12e-01 100.0% 97.4%
4015847 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.81 75.0 4.85e-01 100.0% 47.6%
2757010 1.1.1.4 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Spuma_A9PTase 0.80 70.0 7.18e-01 97.9% 97.8%
3504655 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.80 72.0 6.78e-01 96.9% 90.4%
2543743 1.1.1.3 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP 0.80 74.0 7.17e-01 100.0% 96.2%
4969397 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.80 72.0 6.76e-01 96.9% 93.0%
3929267 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.80 70.0 6.54e-01 95.9% 84.2%
5001647 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.79 67.0 6.45e-01 90.7% 99.1%
3320001 1.1.1.10 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › TAXi_N 0.79 73.0 6.22e-01 100.0% 88.7%
3658254 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.79 71.0 7.04e-01 96.9% 100.0%
3782336 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.78 68.0 6.12e-01 93.8% 76.9%
4436288 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.78 69.0 6.63e-01 94.8% 87.3%
3737912 1.1.1.13 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Peptidase_A2_2 0.78 68.0 6.78e-01 93.8% 100.0%
4027119 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.78 71.0 6.36e-01 100.0% 91.9%
4395060 1.1.1.1 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.78 68.0 6.33e-01 93.8% 98.3%
17 1.1.1.5 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Zn_protease 0.77 72.0 6.52e-01 100.0% 93.7%
3668951 1.1.1.17 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › RVP_2 0.77 61.0 6.32e-01 83.5% 100.0%
4026589 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.77 68.0 5.51e-01 96.9% 96.7%
3541617 1.1.1.6 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease 0.75 66.0 6.15e-01 94.8% 81.7%
3912599 1.1.1.8 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › gag-asp_proteas 0.74 65.0 6.04e-01 94.8% 84.2%
3846274 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.72 63.0 5.96e-01 94.8% 86.1%
D2 high residues 386-464
PDB
Domain cluster: rep: p66_subunit__NP_705927__Human_immunodeficiency_virus_1__11676__D252-315
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF06817.20 best RVT_thumb 86.8 9.80e-25 81.0% 98.5%
D3 high residues 473-563
PDB
Domain cluster: rep: p15NC-p14PR-p95RT_IN__NP_955619__Human_T-cell_leukemia_virus_type_I__11908__D551-648
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF06815.20 best RVT_connect 138.2 1.20e-40 100.0% 88.2%
D4 high residues 577-700
PDB
Domain cluster: rep: polyprotein__YP_002916057__Sweet_potato_badnavirus_B__647294__D493-623
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00075.31 best RNase_H 113.4 1.30e-32 95.2% 94.3%
D5 high residues 767-917
PDB
Domain cluster: rep: AB916497.1__BAS32805.1__X__00007__D17-171
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00665.33 best rve 55.3 9.60e-15 57.0% 94.1%
D6 high residues 923-976
PDB
Domain cluster: rep: integrase__YP_001856243__Human_immunodeficiency_virus_1__11676__D216-264
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00552.28 best IN_DBD_C 76.9 7.90e-22 81.5% 100.0%
D7 medium residues 150-237_263-301
PDB
Domain cluster: rep: pol_protein,_partial__YP_002308474__Simian_T-cell_lymphotropic_virus_6__481147__D16-81_108-143
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00078.33 best RVT_1 30.1 6.10e-07 32.3% 23.0%
D8 medium residues 238-262_302-382
PDB
Domain cluster: rep: hypothetical_protein_2__YP_009345057__Xinzhou_nematode_virus_7__1923775__D238-258_337-401
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00078.33 best RVT_1 53.5 4.00e-14 96.2% 46.5%
D9 medium residues 711-746
PDB