Back to structures

IMGVR_UViG_2554235474_000003-2554235474-2556086875

Arc-Vir

IMGVR_UViG_2554235474_000003-2554235474-2556086875

Identity

Kingdom:
archaea

Quality

83.2 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 11-188
PDB
CATH (33)
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 0.74 56.0 5.08e-01 96.1% 58.9%
3h20A02 3.30.70.1790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RepB DNA-primase, N-terminal domain 0.73 42.0 5.35e-01 95.5% 96.1%
2iruA02 3.30.70.3300 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.73 55.0 6.21e-01 89.9% 100.0%
5of3A00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.71 65.0 5.22e-01 96.1% 62.4%
2atzA00 3.90.920.20 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › HP0184-like 0.71 44.0 4.49e-01 99.4% 63.1%
4bpuC00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.70 66.0 5.09e-01 100.0% 75.5%
2faoA01 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.67 63.0 5.35e-01 100.0% 70.9%
4limA00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.67 62.0 4.80e-01 100.0% 76.9%
2xhcA01 3.30.70.940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain 0.64 34.0 4.51e-01 92.1% 95.8%
3jtnB00 3.30.70.1950 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 34.0 4.57e-01 83.1% 100.0%
4mt1A02 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.61 36.0 4.59e-01 96.6% 100.0%
1z1dB00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.61 37.0 4.23e-01 100.0% 80.2%
5t0oA02 3.30.70.1430 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.60 36.0 4.49e-01 96.6% 100.0%
2abyA00 3.30.70.1980 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Uncharacterised protein PF09406, DUF2004 0.60 36.0 4.25e-01 90.4% 86.1%
1ybtB00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.57 34.0 3.53e-01 96.1% 59.9%
2qyxB01 3.30.70.1360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › mj0159-like 0.57 34.0 4.27e-01 86.0% 98.2%
2wz1B00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.56 39.0 3.85e-01 94.9% 63.3%
6yiiA02 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.55 41.0 3.89e-01 96.6% 63.6%
3otdA00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.55 49.0 4.46e-01 97.2% 91.7%
1sjrA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.55 34.0 4.16e-01 92.7% 100.0%
1r89A03 3.30.70.590 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Poly(A) polymerase predicted RNA binding domain 0.55 37.0 4.21e-01 94.9% 91.8%
4er8A00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.55 41.0 4.23e-01 97.8% 84.2%
4kw3A00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.54 47.0 4.14e-01 94.4% 94.7%
3fnbA01 1.20.1440.110 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › acylaminoacyl peptidase 0.54 30.0 3.57e-01 93.8% 81.6%
2w01B00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.53 37.0 3.58e-01 95.5% 62.4%
1azsA00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.53 36.0 3.53e-01 94.4% 62.1%
2d3aA02 3.30.590.10 Alpha Beta › 2-Layer Sandwich › Creatine Kinase; Chain A, domain 2 › Glutamine synthetase/guanido kinase, catalytic domain 0.52 38.0 3.36e-01 72.5% 79.0%
1ab8A00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.52 37.0 3.80e-01 80.9% 72.9%
1m55A00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.52 44.0 4.34e-01 92.1% 94.8%
3eoqA01 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.52 36.0 3.44e-01 70.8% 89.1%
1p50A02 3.30.590.10 Alpha Beta › 2-Layer Sandwich › Creatine Kinase; Chain A, domain 2 › Glutamine synthetase/guanido kinase, catalytic domain 0.51 36.0 3.23e-01 70.8% 77.3%
3r5gA00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.51 36.0 3.57e-01 94.4% 65.1%
3d3yA01 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.51 39.0 3.59e-01 79.8% 93.6%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5081312 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.84 67.0 6.19e-01 100.0% 66.8%
4426711 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.79 63.0 5.48e-01 96.1% 57.6%
4946939 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.76 61.0 5.86e-01 96.1% 74.0%
4998612 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.75 62.0 5.51e-01 95.5% 63.3%
4274062 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.74 61.0 5.38e-01 96.1% 60.8%
4650634 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.74 59.0 5.25e-01 96.1% 59.2%
4955551 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.74 62.0 5.51e-01 100.0% 63.3%
4983703 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.73 63.0 5.44e-01 100.0% 60.8%
4425840 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.72 66.0 5.30e-01 96.1% 75.3%
5065288 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.71 62.0 5.24e-01 96.1% 58.5%
4212379 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.71 65.0 5.69e-01 96.1% 67.5%
4554731 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.71 59.0 5.40e-01 97.2% 67.4%
5000831 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.71 67.0 5.67e-01 100.0% 67.3%
5019731 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.70 64.0 5.18e-01 96.1% 74.7%
4994656 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.70 64.0 5.57e-01 96.1% 67.3%
3518002 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.70 66.0 5.30e-01 100.0% 69.8%
5050906 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.70 65.0 5.32e-01 100.0% 80.6%
5000686 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.69 63.0 5.29e-01 96.1% 68.4%
4940975 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.69 65.0 5.41e-01 100.0% 61.7%
4993038 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.69 62.0 5.32e-01 96.1% 63.3%
3591528 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.69 65.0 5.47e-01 100.0% 71.9%
3266917 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.69 65.0 5.24e-01 100.0% 65.2%
4442634 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.69 63.0 5.24e-01 96.1% 73.4%
3959043 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.69 65.0 5.21e-01 100.0% 61.5%
4984518 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.69 62.0 5.35e-01 100.0% 63.3%
4946875 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.68 62.0 5.37e-01 96.1% 66.0%
4987159 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.68 64.0 5.58e-01 100.0% 70.8%
4956744 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.68 62.0 5.41e-01 96.1% 70.6%
None 0.68 64.0 5.21e-01 100.0% 64.2%
3692641 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.68 63.0 5.36e-01 100.0% 67.1%
3604598 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.67 64.0 5.38e-01 100.0% 85.0%
3921299 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.67 63.0 5.16e-01 100.0% 68.7%
3278096 862.1.1.5 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.67 63.0 5.10e-01 100.0% 63.1%
4997193 862.1.1.1 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › DNA_primase_S 0.66 58.0 5.10e-01 95.5% 65.6%
None 0.66 62.0 5.04e-01 100.0% 65.2%
4517135 304.41.1.1 a+b two layers › Alpha-beta plaits › Glutamyl tRNA-reductase catalytic, N-terminal domain › Glutamyl tRNA-reductase catalytic, N-terminal domain › GlutR_N 0.62 46.0 4.63e-01 96.1% 77.7%
4387185 304.41.1.1 a+b two layers › Alpha-beta plaits › Glutamyl tRNA-reductase catalytic, N-terminal domain › Glutamyl tRNA-reductase catalytic, N-terminal domain › GlutR_N 0.60 46.0 4.71e-01 97.2% 83.5%
5009932 131.1.1.0 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like 0.60 45.0 3.61e-01 78.7% 98.1%
4215509 304.41.1.1 a+b two layers › Alpha-beta plaits › Glutamyl tRNA-reductase catalytic, N-terminal domain › Glutamyl tRNA-reductase catalytic, N-terminal domain › GlutR_N 0.59 43.0 4.55e-01 95.5% 83.7%
3640423 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 0.57 51.0 4.51e-01 97.2% 93.8%
None 0.57 39.0 3.86e-01 94.9% 63.3%
3412446 304.48.1.4 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Guanylate_cyc 0.56 38.0 3.37e-01 94.9% 46.3%
4269228 304.122.1.1 a+b two layers › Alpha-beta plaits › Nitrogen repressor-like proteins › Nitrogen repressor-like proteins › NRD1_2 0.55 34.0 4.23e-01 86.5% 100.0%
3826050 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 0.54 48.0 4.22e-01 98.3% 92.0%
3999306 304.48.1.4 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Guanylate_cyc 0.54 38.0 3.57e-01 94.4% 57.7%
3615693 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.53 38.0 3.56e-01 95.5% 58.6%
None 0.52 39.0 2.82e-01 94.9% 25.9%
147149 304.48.1.4 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Guanylate_cyc 0.51 36.0 3.57e-01 94.4% 65.1%
3787014 309.1.1.2 a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16,Peptidase_M16_C 0.51 36.0 3.34e-01 70.2% 84.4%
3971634 304.6.1.0 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain 0.51 39.0 3.90e-01 92.1% 77.1%
D2 high residues 194-336
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3dA03 1.10.579.10 Mainly Alpha › Orthogonal Bundle › DNA Cyclobutane Dipyrimidine Photolyase, subunit A; domain 3 › DNA Cyclobutane Dipyrimidine Photolyase, subunit A, domain 3 0.74 58.0 5.26e-01 82.5% 73.2%
3lcnB00 1.10.340.40 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain 0.68 32.0 3.84e-01 79.0% 64.9%
2mbgA01 1.10.555.10 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase; Chain A › Rho GTPase activation protein 0.56 40.0 3.56e-01 72.7% 76.9%
4z4qA04 1.10.268.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 0.55 28.0 3.45e-01 91.6% 75.3%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4494836 182.1.3.3 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.81 56.0 5.90e-01 72.7% 76.9%
5068030 182.1.3.3 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.80 55.0 5.99e-01 74.1% 83.3%
4978272 182.1.3.3 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.79 55.0 6.11e-01 74.8% 87.8%
4970738 182.1.3.3 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.79 56.0 6.07e-01 72.0% 85.8%
4103318 182.1.2.1 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › Fe-S cluster domain of DNA primase › DNA_primase_lrg 0.79 56.0 5.79e-01 74.1% 77.0%
4935112 182.1.3.3 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.78 56.0 6.07e-01 74.1% 86.7%
5028655 182.1.3.3 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.78 54.0 5.91e-01 71.3% 86.7%
5043574 182.1.3.3 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.77 54.0 5.81e-01 74.1% 81.6%
5049375 182.1.2.1 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › Fe-S cluster domain of DNA primase › DNA_primase_lrg 0.76 54.0 5.63e-01 74.8% 77.8%
5057453 182.1.3.3 alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.74 56.0 6.00e-01 88.8% 89.6%
3813149 5059.1.1.3 alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › TPT 0.62 43.0 3.34e-01 70.6% 83.8%
3964803 5059.1.1.1 alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.52 42.0 3.29e-01 84.6% 76.9%
5053127 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 42.0 3.29e-01 89.5% 46.9%
3514598 7525.1.1.2 a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_2 0.51 37.0 2.85e-01 76.9% 82.2%