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putative_5-3--deoxyribonucleotidase
Euk-VirAcanthamoeba_polyphaga_mimivirus
putative_5-3--deoxyribonucleotidase__YP_003987288__Acanthamoeba_polyphaga_mimivirus__212035
Identity
- Accession:
- YP_003987288 ↗
- Protein ID:
- putative_5-3--deoxyribonucleotidase
- Kingdom:
- euk
Quality
76.9
mean pLDDT
Taxonomy
Bamfordvirae›
Nucleocytoviricota›
Megaviricetes›
Imitervirales›
Mimiviridae›
Mimivirus›
Acanthamoeba_polyphaga_mimivirus
TaxID: 212035
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
medium
residues 6-30_51-64_118-183
Domain cluster:
representative
CATH (17)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3d6jA01 | 3.40.50.1000 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like | 0.60 | 47.0 | 4.16e-01 | 81.9% | 100.0% |
| 3s6jA01 | 3.40.50.1000 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like | 0.59 | 51.0 | 4.49e-01 | 92.4% | 100.0% |
| 2c4nA01 | 3.40.50.1000 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like | 0.59 | 48.0 | 4.25e-01 | 85.7% | 100.0% |
| 3kc2A01 | 3.40.50.1000 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like | 0.58 | 51.0 | 4.32e-01 | 92.4% | 100.0% |
| 1wv8A00 | 3.30.2390.10 | Alpha Beta › 2-Layer Sandwich › TTHA1013/TTHA0281-like › TTHA1013-like | 0.57 | 32.0 | 3.69e-01 | 92.4% | 77.5% |
| 1vjrA01 | 3.40.50.1000 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like | 0.57 | 47.0 | 4.10e-01 | 86.7% | 97.4% |
| 3qgmA01 | 3.40.50.1000 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like | 0.56 | 46.0 | 3.91e-01 | 85.7% | 99.4% |
| 2hjjA00 | 3.30.160.130 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › ykff protein like domains | 0.55 | 32.0 | 3.89e-01 | 72.4% | 90.9% |
| 5gu6A02 | 3.40.30.10 | Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin | 0.55 | 41.0 | 4.23e-01 | 89.5% | 83.2% |
| 3kzxA01 | 3.40.50.1000 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like | 0.55 | 48.0 | 4.34e-01 | 92.4% | 100.0% |
| 2a9sB00 | 3.90.950.20 | Alpha Beta › Alpha-Beta Complex › Maf protein › CinA-like | 0.55 | 48.0 | 4.18e-01 | 97.1% | 92.7% |
| 3mixA01 | 3.40.30.60 | Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › FHIPEP family, domain 1 | 0.55 | 44.0 | 4.26e-01 | 88.6% | 76.7% |
| 3uh0A02 | 3.40.50.800 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain | 0.54 | 48.0 | 4.53e-01 | 97.1% | 95.2% |
| 3qkwB01 | 3.40.50.2000 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; | 0.54 | 46.0 | 3.89e-01 | 93.3% | 100.0% |
| 2b5eA02 | 3.40.30.10 | Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin | 0.53 | 39.0 | 4.01e-01 | 86.7% | 82.5% |
| 3k1lA02 | 3.30.457.30 | Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › | 0.52 | 36.0 | 3.81e-01 | 71.4% | 91.1% |
| 4qjiB00 | 3.40.50.10300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › CoaB-like | 0.51 | 44.0 | 3.53e-01 | 97.1% | 99.1% |
ECOD (17)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3689413 | 2485.1.1.0 ↗ | a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like | 0.61 | 49.0 | 4.45e-01 | 86.7% | 80.0% |
| 4929701 | 4100.1.1.0 ↗ | a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like | 0.60 | 33.0 | 4.15e-01 | 94.3% | 93.3% |
| 3977758 | 2006.1.1.16 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase_like,Hydrolase_6 | 0.59 | 48.0 | 4.23e-01 | 84.8% | 99.3% |
| 5057703 | 2006.1.1.15 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase_like | 0.58 | 47.0 | 4.15e-01 | 84.8% | 97.9% |
| 3166135 | 4312.1.1.4 ↗ | a+b two layers › RelE-like › RelE-like › RelE-like › Gp49 | 0.57 | 32.0 | 3.36e-01 | 81.9% | 58.9% |
| 3716915 | 2006.1.1.16 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Hydrolase_like,Hydrolase_6 | 0.56 | 45.0 | 3.78e-01 | 84.8% | 90.8% |
| 3781695 | 2485.1.1.87 ↗ | a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › UBX7_N | 0.56 | 45.0 | 4.33e-01 | 87.6% | 80.0% |
| 3838066 | 7520.1.1.1 ↗ | a/b three-layered sandwiches › CinA-like › CinA-like › CinA-like › CinA | 0.56 | 48.0 | 4.24e-01 | 96.2% | 95.6% |
| 4431310 | 7520.1.1.1 ↗ | a/b three-layered sandwiches › CinA-like › CinA-like › CinA-like › CinA | 0.55 | 49.0 | 4.22e-01 | 99.0% | 93.9% |
| 3613037 | 2004.1.1.208 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_33 | 0.53 | 45.0 | 3.43e-01 | 94.3% | 95.8% |
| 4384861 | 2004.1.1.14 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › GTP_EFTU | 0.53 | 44.0 | 3.15e-01 | 94.3% | 83.8% |
| 6667 | 4221.1.1.1 ↗ | a+b two layers › YkuJ-like › YkuJ-like › YkuJ-like › DUF1797 | 0.52 | 34.0 | 3.85e-01 | 87.6% | 89.7% |
| 3359263 | 2003.1.1.186 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › DUF7870 | 0.52 | 28.0 | 2.69e-01 | 93.3% | 40.8% |
| 4559415 | 2004.1.1.0 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases | 0.52 | 45.0 | 2.95e-01 | 96.2% | 62.2% |
| 3486916 | 2485.1.1.0 ↗ | a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like | 0.51 | 42.0 | 4.35e-01 | 96.2% | 100.0% |
| 3300200 | 220.1.1.0 ↗ | beta barrels › PH domain-like › PH domain-like › PH domain-like | 0.51 | 30.0 | 2.85e-01 | 90.5% | 45.2% |
| 3530175 | 2485.1.1.40 ↗ | a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › GST_N_3 | 0.50 | 40.0 | 3.87e-01 | 93.3% | 76.7% |
D2
medium
residues 31-50_65-117
Domain cluster:
representative
CATH (25)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1z4mA01 | 3.40.50.1000 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like | 0.78 | 61.0 | 4.77e-01 | 80.8% | 48.2% |
| 6p4xA03 | 3.40.367.20 | Alpha Beta › 3-Layer(aba) Sandwich › Hexokinase; domain 1 › | 0.61 | 53.0 | 3.60e-01 | 98.6% | 62.9% |
| 4y9tA02 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.61 | 49.0 | 3.66e-01 | 86.3% | 46.0% |
| 4obxA00 | 3.40.50.150 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 | 0.60 | 47.0 | 3.30e-01 | 84.9% | 43.4% |
| 3ty4B00 | 3.40.718.10 | Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase | 0.59 | 51.0 | 3.33e-01 | 100.0% | 40.1% |
| 4wzzA02 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.58 | 46.0 | 3.64e-01 | 89.0% | 49.1% |
| 3bq9A02 | 3.40.50.450 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.57 | 49.0 | 3.20e-01 | 97.3% | 51.8% |
| 1xknA00 | 3.75.10.10 | Alpha Beta › 5-stranded Propeller › L-arginine/glycine Amidinotransferase; Chain A › L-arginine/glycine Amidinotransferase; Chain A | 0.57 | 48.0 | 3.10e-01 | 93.2% | 34.6% |
| 4f3nA00 | 3.40.50.12710 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.57 | 48.0 | 3.05e-01 | 93.2% | 29.1% |
| 2grvC03 | 3.10.105.10 | Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 | 0.57 | 46.0 | 3.29e-01 | 90.4% | 65.2% |
| 3ocjA00 | 3.40.50.150 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 | 0.56 | 46.0 | 3.05e-01 | 90.4% | 41.0% |
| 3a43A01 | 3.30.2320.50 | Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › | 0.56 | 41.0 | 4.05e-01 | 79.5% | 93.7% |
| 1jeyB01 | 3.40.50.410 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain | 0.56 | 48.0 | 3.47e-01 | 100.0% | 66.1% |
| 5bq3A02 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.55 | 44.0 | 3.50e-01 | 89.0% | 51.0% |
| 2zc1A00 | 3.20.20.140 | Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases | 0.55 | 47.0 | 3.08e-01 | 95.9% | 66.4% |
| 1vbkA03 | 3.40.50.620 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs | 0.54 | 44.0 | 3.60e-01 | 87.7% | 48.1% |
| 3oa3A00 | 3.20.20.70 | Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I | 0.54 | 46.0 | 3.21e-01 | 95.9% | 55.3% |
| 4hh4C01 | 3.40.50.150 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 | 0.54 | 44.0 | 3.33e-01 | 93.2% | 52.6% |
| 3fg6A01 | 3.40.20.10 | Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin | 0.54 | 44.0 | 4.02e-01 | 91.8% | 79.8% |
| 1wy5A01 | 3.40.50.620 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs | 0.54 | 40.0 | 2.90e-01 | 80.8% | 41.0% |
| 7vevA01 | 3.10.105.10 | Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 | 0.53 | 45.0 | 3.20e-01 | 97.3% | 62.5% |
| 1ycdB00 | 3.40.50.1820 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain | 0.53 | 45.0 | 3.25e-01 | 100.0% | 60.5% |
| 4fcyA01 | 1.10.10.60 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like | 0.52 | 36.0 | 3.57e-01 | 72.6% | 78.2% |
| 3v7nA02 | 3.40.50.1100 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.52 | 45.0 | 3.29e-01 | 100.0% | 85.5% |
| 2py6A03 | 3.40.50.150 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 | 0.52 | 44.0 | 3.34e-01 | 95.9% | 50.0% |
ECOD (32)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3868100 | 2006.1.1.10 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › NT5C | 0.77 | 71.0 | 5.07e-01 | 100.0% | 50.5% |
| 1144914 | 2006.1.1.10 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › NT5C | 0.77 | 71.0 | 5.09e-01 | 100.0% | 51.5% |
| 4188249 | 2006.1.1.10 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › NT5C | 0.77 | 71.0 | 5.18e-01 | 100.0% | 53.9% |
| 5018983 | 2006.1.1.10 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › NT5C | 0.72 | 65.0 | 4.83e-01 | 100.0% | 54.4% |
| 4945339 | 2484.1.1.0 ↗ | mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like | 0.59 | 51.0 | 3.93e-01 | 97.3% | 76.5% |
| 3720168 | 2005.2.1.0 ↗ | a/b three-layered sandwiches › HUP domain-like › YdcF › YdcF | 0.57 | 49.0 | 3.42e-01 | 95.9% | 66.3% |
| 3248152 | 7512.1.1.3 ↗ | a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glycos_transf_1 | 0.57 | 47.0 | 3.36e-01 | 93.2% | 38.2% |
| 5036317 | 2005.1.1.7 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d | 0.56 | 46.0 | 3.02e-01 | 91.8% | 64.8% |
| 4020312 | 2005.1.1.7 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d | 0.56 | 45.0 | 3.13e-01 | 91.8% | 73.7% |
| 5044620 | 2003.1.5.81 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 | 0.56 | 45.0 | 3.34e-01 | 93.2% | 48.4% |
| 1674673 | 2007.1.2.11 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › Peripla_BP_4 | 0.56 | 42.0 | 3.48e-01 | 83.6% | 56.5% |
| 2489493 | 2005.1.1.7 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d | 0.55 | 44.0 | 2.95e-01 | 91.8% | 65.2% |
| 4021476 | 7512.1.1.0 ↗ | a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase | 0.55 | 45.0 | 3.29e-01 | 93.2% | 40.5% |
| 3932457 | 2005.1.1.7 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d | 0.55 | 46.0 | 3.09e-01 | 94.5% | 72.8% |
| None | — | 0.54 | 47.0 | 3.43e-01 | 100.0% | 43.8% | |
| 3503160 | 7512.1.1.3 ↗ | a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glycos_transf_1 | 0.54 | 44.0 | 3.21e-01 | 93.2% | 40.5% |
| None | — | 0.53 | 46.0 | 3.39e-01 | 100.0% | 62.9% | |
| 4020807 | 2005.1.1.0 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains | 0.53 | 44.0 | 2.95e-01 | 93.2% | 87.7% |
| 4991101 | 7523.1.1.0 ↗ | a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II | 0.53 | 42.0 | 3.01e-01 | 94.5% | 65.2% |
| 3479455 | 7512.1.1.3 ↗ | a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glycos_transf_1 | 0.53 | 43.0 | 3.18e-01 | 93.2% | 39.5% |
| 3730592 | 2005.1.1.7 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d | 0.53 | 44.0 | 2.93e-01 | 93.2% | 91.1% |
| None | — | 0.52 | 43.0 | 2.95e-01 | 94.5% | 41.8% | |
| 3501422 | 7512.1.1.3 ↗ | a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glycos_transf_1 | 0.51 | 41.0 | 3.07e-01 | 91.8% | 36.2% |
| 4658028 | 140.1.1.0 ↗ | alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.51 | 44.0 | 2.61e-01 | 98.6% | 64.1% |
| 5031492 | 3008.1.1.2 ↗ | a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DUF5915 | 0.51 | 39.0 | 3.75e-01 | 86.3% | 76.7% |
| 5066822 | 2005.1.1.124 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › DALR_1 | 0.51 | 44.0 | 2.61e-01 | 98.6% | 61.9% |
| 3728192 | 2003.1.1.22 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › GFO_IDH_MocA | 0.51 | 41.0 | 3.36e-01 | 93.2% | 48.7% |
| 5009361 | 2007.1.14.0 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like | 0.51 | 43.0 | 3.63e-01 | 95.9% | 80.5% |
| 4951092 | 2007.1.5.2 ↗ | a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › ATC-like › CCG | 0.51 | 42.0 | 3.15e-01 | 98.6% | 94.0% |
| 4978050 | 2005.1.1.0 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains | 0.50 | 43.0 | 2.61e-01 | 97.3% | 78.0% |
| 3739965 | 298.1.1.0 ↗ | a+b two layers › FwdE/GAPDH domain-like › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 0.50 | 41.0 | 2.66e-01 | 93.2% | 19.5% |
| 3554460 | 328.1.1.3 ↗ | a+b two layers › IF3-like › AlbA-like › AlbA-like › Rpp20 | 0.50 | 38.0 | 3.46e-01 | 84.9% | 70.5% |