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DNA_ligase

Euk-Vir

Anopheles_minimus_iridovirus

DNA_ligase__YP_009021193__Anopheles_minimus_iridovirus__1465751

Identity

Accession:: YP_009021193 ↗
Protein ID:: DNA_ligase
Kingdom:: euk

Quality

80.7 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Iridoviridae› Chloriridovirus› Chloriridovirus_anopheles1

TaxID: 1465751

Cluster

View cluster (18 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 9-59

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF22745.3 best	Nlig-Ia	28.9	1.20e-06	96.1%	61.9%

CATH (13)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1vq8V00	1.10.287.310	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.84	65.0	6.01e-01	88.2%	66.2%
1p49A02	1.10.287.550	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin	0.78	59.0	5.72e-01	86.3%	72.9%
1b04A03	1.10.287.610	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin	0.77	67.0	6.29e-01	96.1%	95.2%
7dukB01	1.10.287.610	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin	0.76	54.0	5.65e-01	76.5%	100.0%
1x4tA01	1.10.287.660	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin	0.73	58.0	5.59e-01	88.2%	82.8%
2q0oC00	1.10.287.160	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat	0.71	54.0	4.67e-01	86.3%	52.3%
6xkyA01	1.20.1330.10	Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain	0.71	60.0	4.11e-01	98.0%	49.2%
4id0A02	1.20.1050.10	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.66	55.0	4.44e-01	100.0%	49.1%
4toiA02	1.10.287.610	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin	0.66	55.0	5.67e-01	94.1%	100.0%
2uv8A07	6.10.140.1410	Special › Helix non-globular › Helix Hairpins ›	0.61	46.0	3.89e-01	82.4%	50.6%
2dk8A01	1.10.10.10	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	0.60	47.0	4.41e-01	88.2%	75.4%
2f6uA00	3.20.20.390	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › FMN-linked oxidoreductases	0.59	50.0	3.21e-01	92.2%	56.7%
3jtgA01	1.10.10.10	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	0.57	43.0	3.68e-01	84.3%	97.6%

ECOD (25)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4541712	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.88	81.0	4.87e-01	100.0%	45.8%
4566687	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.88	81.0	4.80e-01	100.0%	62.5%
4064364	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.88	81.0	4.82e-01	100.0%	18.7%
3840047	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.88	81.0	4.85e-01	100.0%	94.8%
4463257	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.87	79.0	4.75e-01	100.0%	68.1%
4160069	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.87	78.0	4.67e-01	98.0%	19.0%
4556311	206.1.3.5 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › DNA_ligase_aden	0.86	76.0	4.61e-01	96.1%	18.6%
4265994	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.86	78.0	4.69e-01	100.0%	47.1%
4009355	206.1.3.5 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › DNA_ligase_aden	0.86	76.0	4.63e-01	98.0%	18.6%
4043670	192.4.1.26 ↗	alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Nlig-Ia	0.86	76.0	6.63e-01	98.0%	78.7%
None	—		0.85	76.0	4.62e-01	98.0%	19.0%
4432215	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.85	78.0	4.68e-01	100.0%	94.2%
4143426	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.85	77.0	4.60e-01	100.0%	95.3%
4208015	192.4.1.26 ↗	alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Nlig-Ia	0.85	73.0	6.54e-01	94.1%	77.1%
4287728	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.84	73.0	4.35e-01	94.1%	16.9%
4281635	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.84	75.0	4.50e-01	100.0%	19.4%
4119003	206.1.3.5 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › DNA_ligase_aden	0.82	75.0	4.53e-01	100.0%	38.7%
4296465	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.82	74.0	4.48e-01	100.0%	96.8%
None	—		0.81	62.0	3.50e-01	86.3%	7.9%
4010395	622.4.1.26 ↗	alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › HisKA	0.75	60.0	5.40e-01	88.2%	68.6%
3982421	605.1.1.1 ↗	alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA	0.75	60.0	5.27e-01	88.2%	64.0%
4964664	605.1.1.1 ↗	alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA	0.72	56.0	5.22e-01	86.3%	92.3%
3473900	364.1.1.1 ↗	few secondary structure elements › TAZ domain › TAZ domain › TAZ domain › zf-TAZ	0.65	57.0	4.74e-01	100.0%	98.9%
3234298	192.29.1.0 ↗	alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding)	0.64	49.0	4.89e-01	88.2%	87.3%
3415935	103.1.1.0 ↗	alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain	0.63	47.0	4.86e-01	88.2%	100.0%

D2 high residues 547-619

PDB

Domain cluster: rep: MN095770.1__QFR57709.1__CPT_Slocum_152__00129__D178-251

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00533.34 best	BRCT	30.7	3.90e-07	94.5%	87.2%

D3 medium residues 60-71_107-231

PDB

Domain cluster: rep: ATP-dependent_DNA_ligase__YP_009094561__Melbournevirus__1560514__D164-283

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01653.24 best	DNA_ligase_aden	41.8	1.30e-10	97.1%	54.9%

D4 medium residues 72-106_232-291

PDB

Domain cluster: rep: ON649702__UVF62572.1__X__00095__D231-262_382-434

D5 medium residues 292-386

PDB

Domain cluster: rep: LC680885.1__BDE75744.1__X__00206__D318-424

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03120.23 best	OB_DNA_ligase	48.6	9.00e-13	82.1%	93.7%

D6 medium residues 437-535

PDB

Domain cluster: representative

CATH (13)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2m6uA00	1.20.81.20	Mainly Alpha › Up-down Bundle › Receptor-associated Protein ›	0.63	30.0	3.23e-01	75.8%	52.4%
1g4uS01	1.20.120.260	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Virulence factor YopE uncharacterised domain	0.58	39.0	3.58e-01	79.8%	53.5%
2jbrA01	1.10.540.10	Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain	0.56	28.0	2.68e-01	76.8%	37.8%
4g84A01	3.30.930.10	Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2	0.56	43.0	3.05e-01	84.8%	49.2%
2datA00	1.20.920.10	Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like	0.56	38.0	3.58e-01	70.7%	90.2%
1w3iA00	3.20.20.70	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I	0.55	40.0	2.96e-01	84.8%	26.3%
6wlvB01	1.10.287.70	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.55	46.0	3.54e-01	96.0%	40.9%
4bofA02	1.10.3930.10	Mainly Alpha › Orthogonal Bundle › Pentein › Arginine deiminase	0.55	29.0	3.08e-01	77.8%	55.2%
1gvnA00	1.10.8.130	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 ›	0.52	31.0	3.33e-01	92.9%	67.8%
4gkfA00	1.10.520.30	Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › AF1862-like domain	0.52	39.0	3.44e-01	79.8%	86.3%
1gt0D00	1.10.30.10	Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain	0.51	33.0	3.66e-01	78.8%	82.3%
2ozbB01	1.10.287.4070	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.51	40.0	3.68e-01	84.8%	96.2%
3amjB01	3.30.830.10	Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like	0.50	35.0	2.83e-01	73.7%	63.0%

ECOD (8)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3945769	3759.1.1.1 ↗	alpha arrays › Antitermination protein Q helical domain › Antitermination protein Q helical domain › Antitermination protein Q helical domain › Antiterm	0.63	47.0	4.30e-01	79.8%	89.6%
3986535	3759.1.1.1 ↗	alpha arrays › Antitermination protein Q helical domain › Antitermination protein Q helical domain › Antitermination protein Q helical domain › Antiterm	0.63	47.0	4.05e-01	79.8%	74.4%
5008654	5069.1.1.26 ↗	alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › NrfD	0.59	40.0	3.98e-01	80.8%	65.7%
3788512	129.1.1.11 ↗	alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › ApbA_C	0.57	36.0	3.17e-01	77.8%	41.3%
3575635	4044.1.1.0 ↗	alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins	0.57	34.0	3.60e-01	73.7%	64.4%
4015729	192.7.1.0 ↗	alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm	0.54	42.0	3.89e-01	82.8%	66.4%
4229822	192.7.1.3 ↗	alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Phe_tRNA-synt_N	0.53	33.0	3.62e-01	74.7%	77.5%
4144086	166.1.1.1 ↗	alpha superhelices › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › 1-deoxy-D-xylulose-5-phosphate reductoisomerase-C › DXPR_C	0.52	26.0	2.64e-01	92.9%	45.0%