Back to structures

IMGVR_UViG_2502082094_000001-2502082094-2502095210

Arc-Vir

IMGVR_UViG_2502082094_000001-2502082094-2502095210

Identity

Kingdom:
archaea

Quality

79.8 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 304-383
PDB
D2 medium residues 1-17_114-278
PDB
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1g71A01 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.79 49.0 4.43e-01 74.7% 48.3%
3h20A02 3.30.70.1790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RepB DNA-primase, N-terminal domain 0.79 44.0 5.89e-01 79.1% 99.0%
2iruA02 3.30.70.3300 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.71 49.0 5.55e-01 74.2% 91.3%
1z1dB00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.68 39.0 4.52e-01 78.6% 77.1%
2a10D00 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.66 38.0 4.90e-01 78.0% 100.0%
1m55A00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.64 48.0 4.69e-01 75.8% 87.6%
1r89A03 3.30.70.590 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Poly(A) polymerase predicted RNA binding domain 0.64 41.0 4.68e-01 74.7% 85.8%
4kgmA00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.63 47.0 4.35e-01 77.5% 90.9%
4er8A00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.59 42.0 4.44e-01 76.9% 80.0%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.59 44.0 4.08e-01 78.0% 85.4%
2av5A00 3.30.70.3250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribonuclease P, Pop5 subunit 0.59 35.0 4.36e-01 71.4% 99.1%
4yubB01 3.20.140.10 Alpha Beta › Alpha-Beta Barrel › nicotinate phosphoribosyltransferase › nicotinate phosphoribosyltransferase 0.55 42.0 3.60e-01 79.1% 73.2%
4fprB00 3.30.70.2910 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 36.0 4.19e-01 77.5% 95.3%
3znuA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.52 28.0 3.71e-01 78.6% 98.9%
2w01B00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.51 44.0 4.29e-01 90.7% 96.4%
1rniA02 3.30.2250.10 Alpha Beta › 2-Layer Sandwich › Prim-pol fold › Bifunctional DNA primase/polymerase domain 0.51 31.0 3.75e-01 88.5% 93.9%
1khvA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.50 35.0 4.07e-01 74.7% 100.0%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5004227 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.84 65.0 5.77e-01 87.9% 58.0%
4554731 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.79 52.0 4.73e-01 74.2% 52.2%
4650634 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.79 52.0 4.61e-01 74.7% 49.2%
4274062 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.77 53.0 4.66e-01 74.7% 50.8%
4962169 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.77 49.0 4.45e-01 74.2% 50.0%
5059790 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.74 64.0 4.87e-01 90.7% 81.2%
5000831 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.72 58.0 4.98e-01 83.0% 68.7%
4989296 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.72 54.0 4.50e-01 75.8% 61.7%
4984518 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.71 59.0 5.11e-01 86.3% 63.7%
4956744 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.71 52.0 4.57e-01 74.7% 62.0%
5026687 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.71 60.0 5.15e-01 88.5% 63.6%
3602638 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.71 53.0 4.07e-01 86.3% 35.2%
4940975 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.71 53.0 4.44e-01 77.5% 59.0%
4955551 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.70 59.0 5.26e-01 87.9% 67.3%
5065288 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.67 52.0 4.42e-01 78.6% 90.9%
5066297 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.67 57.0 4.93e-01 89.0% 70.2%
4993038 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.67 51.0 4.44e-01 78.6% 93.2%
3370992 304.48.1.21 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Thg1,Thg1C 0.63 47.0 3.52e-01 76.9% 51.2%
3249428 304.48.1.20 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Thg1 0.62 47.0 4.10e-01 78.0% 90.2%
4396408 304.20.1.5 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › tRNA_synt_2f 0.61 43.0 4.10e-01 73.1% 99.5%
4964850 304.48.1.22 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › GCH_III 0.60 38.0 4.46e-01 87.9% 90.4%
3715696 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.60 49.0 4.15e-01 84.6% 75.7%
5026874 304.57.1.1 a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.59 37.0 4.51e-01 73.1% 98.3%
4413784 304.57.1.1 a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.58 36.0 4.28e-01 75.3% 91.7%
4092955 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.58 41.0 4.29e-01 71.4% 95.2%
4975149 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.58 32.0 4.09e-01 87.4% 95.0%
4193555 304.57.1.1 a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.57 35.0 4.10e-01 71.4% 88.3%
4976338 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.57 41.0 4.12e-01 74.2% 90.0%
141464 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.57 41.0 4.14e-01 74.2% 87.0%
4943031 304.28.1.38 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › CAA_C 0.56 41.0 4.12e-01 74.2% 88.6%
3604040 304.57.1.1 a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 0.56 35.0 4.03e-01 70.9% 84.3%
5004971 304.28.1.38 a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › CAA_C 0.56 41.0 4.13e-01 74.2% 89.6%
4514959 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.56 41.0 4.09e-01 74.2% 88.6%
5067611 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.56 40.0 3.98e-01 72.5% 86.8%
5071942 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.56 41.0 3.97e-01 74.2% 86.5%
4987404 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.56 40.0 4.02e-01 74.2% 87.4%
5032300 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.55 40.0 3.98e-01 74.2% 88.7%
4992428 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.55 40.0 3.93e-01 74.2% 86.9%
4054591 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.55 40.0 3.99e-01 74.2% 85.3%
5000048 304.20.1.4 a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › CAA_C 0.55 40.0 4.00e-01 74.2% 92.1%
4964645 309.1.1.15 a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › DEAD_assoc 0.54 38.0 3.88e-01 71.4% 88.3%
4931792 306.3.1.6 a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › DEAD_assoc 0.53 37.0 3.68e-01 72.0% 90.3%
D3 medium residues 18-113
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.76 51.0 6.02e-01 93.8% 100.0%
3rgzA02 3.30.1490.310 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.63 38.0 4.53e-01 70.8% 93.4%
1svdM00 3.30.190.10 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribulose bisphosphate carboxylase, small subunit 0.62 48.0 4.68e-01 100.0% 74.1%
5cqgA04 3.30.70.2630 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 44.0 4.27e-01 74.0% 77.4%
1s6lA02 3.15.10.60 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Alkylmercury lyase 0.62 37.0 3.43e-01 70.8% 44.2%
1r9fA01 3.30.390.180 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › RNA silencing suppressor P19 0.61 43.0 4.17e-01 72.9% 66.1%
3l5hA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 43.0 4.77e-01 92.7% 97.4%
1ap8A00 3.30.760.10 Alpha Beta › 2-Layer Sandwich › RNA Cap, Translation Initiation Factor Eif4e › RNA Cap, Translation Initiation Factor Eif4e 0.54 43.0 3.38e-01 87.5% 74.6%
5kfzA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.54 47.0 4.39e-01 99.0% 84.6%
3bdeB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 39.0 3.88e-01 76.0% 100.0%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.52 35.0 3.07e-01 75.0% 44.1%
4hesA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 38.0 2.81e-01 79.2% 28.4%
2z0uA00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.51 41.0 3.80e-01 88.5% 76.6%
2kltA00 2.60.40.2030 Mainly Beta › Sandwich › Immunoglobulin-like › CalX-beta domain 0.50 43.0 3.71e-01 95.8% 78.8%
2a74D01 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.50 37.0 3.40e-01 79.2% 58.6%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3732370 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.67 42.0 5.01e-01 77.1% 100.0%
3634674 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.65 45.0 3.06e-01 71.9% 67.4%
3712786 3346.1.1.0 a+b two layers › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 0.63 46.0 3.76e-01 95.8% 41.7%
3578087 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 39.0 4.32e-01 71.9% 81.3%
4956977 206.1.3.3 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › PPDK_N 0.60 52.0 3.67e-01 97.9% 78.1%
3312666 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.59 41.0 4.62e-01 92.7% 100.0%
3339376 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.58 44.0 4.17e-01 94.8% 67.8%
4237265 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.58 48.0 4.62e-01 90.6% 100.0%
3481162 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 46.0 4.49e-01 97.9% 79.0%
3265985 3529.1.1.0 beta sandwiches › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain › Major vault protein (MVP) structural repeat domain 0.55 30.0 3.84e-01 71.9% 100.0%
3590783 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.54 46.0 4.14e-01 99.0% 67.6%
3215061 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 40.0 3.76e-01 80.2% 72.5%
4981506 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 42.0 4.20e-01 93.8% 81.0%
3427960 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.53 47.0 4.32e-01 97.9% 98.4%
4030767 3504.1.1.1 beta barrels › MutM N-terminal domain-like › Hypothetical protein YojF › Hypothetical protein YojF › DUF1806 0.53 44.0 4.11e-01 91.7% 97.5%
3827630 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.53 37.0 4.00e-01 72.9% 95.0%
3484653 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.53 44.0 4.22e-01 92.7% 79.1%
3397457 379.1.1.0 few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.53 32.0 3.87e-01 75.0% 98.3%
3719864 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 39.0 3.87e-01 80.2% 100.0%
3210219 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 44.0 4.28e-01 94.8% 94.5%
3300115 221.1.1.76 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.51 40.0 3.94e-01 87.5% 99.0%
3824339 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.50 40.0 3.39e-01 86.5% 76.4%
3574350 210.2.1.0 a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain 0.50 41.0 3.20e-01 93.8% 71.1%