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DNA_topoisomerase_IA

Euk-Vir

Chrysochromulina_ericina_virus

DNA_topoisomerase_IA__YP_009173643__Chrysochromulina_ericina_virus__455364

Identity

Accession:: YP_009173643 ↗
Protein ID:: DNA_topoisomerase_IA
Kingdom:: euk

Quality

74.5 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Algavirales› Phycodnaviridae› Chrysochromulina_ericina_virus

TaxID: 455364

Cluster

View cluster (9 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 medium residues 4-127

PDB

Domain cluster: rep: IMGVR_UViG_3300014887_000003-3300014887-Ga0180302_1000002739__D2-143

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01751.29 best	Toprim	74.9	6.40e-21	87.9%	99.0%

D2 medium residues 155-230_465-558

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01131.26 best	Topoisom_bac	52.0	8.40e-14	47.6%	12.9%

CATH (16)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1mw9X02	1.10.460.10	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; domain 2 › Topoisomerase I, domain 2	0.87	50.0	5.13e-01	100.0%	60.1%
1sd4A01	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	0.82	32.0	5.41e-01	82.9%	100.0%
1tbxB00	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	0.80	39.0	5.41e-01	93.5%	90.0%
1p6rA00	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	0.80	37.0	5.37e-01	91.8%	93.9%
2mh2A00	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	0.78	31.0	5.12e-01	81.8%	100.0%
2g9wA01	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	0.78	32.0	5.16e-01	87.6%	100.0%
1s3jA02	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	0.74	30.0	4.83e-01	82.9%	100.0%
3eyyA01	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	0.73	35.0	4.92e-01	89.4%	95.1%
3l09A02	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	0.72	36.0	5.06e-01	91.2%	97.6%
6abqB00	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	0.72	38.0	4.81e-01	93.5%	84.0%
3gw2A00	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	0.71	38.0	5.12e-01	96.5%	95.7%
2fe3B01	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	0.70	33.0	4.66e-01	88.2%	90.6%
2d1hB00	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	0.68	33.0	4.33e-01	94.1%	80.6%
3g2bA00	1.10.10.1150	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Coenzyme PQQ synthesis protein D (PqqD)	0.67	25.0	3.45e-01	88.8%	64.4%
1t0fA02	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	0.58	30.0	3.78e-01	92.9%	83.8%
3i3lA02	3.30.390.160	Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 ›	0.54	29.0	3.36e-01	86.5%	71.2%

ECOD (24)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3614788	2006.1.3.2 ↗	a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › Toprim	0.91	51.0	3.81e-01	100.0%	26.7%
3704475	101.1.2.19 ↗	alpha arrays › HTH › HTH › winged helix domain › Topoisom_bac	0.90	51.0	4.65e-01	100.0%	45.1%
5003642	101.1.2.19 ↗	alpha arrays › HTH › HTH › winged helix domain › Topoisom_bac	0.89	51.0	3.94e-01	100.0%	29.6%
3593805	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.88	52.0	3.83e-01	100.0%	26.2%
4930522	101.1.2.19 ↗	alpha arrays › HTH › HTH › winged helix domain › Topoisom_bac	0.88	51.0	5.00e-01	100.0%	55.0%
4988773	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.88	46.0	4.95e-01	100.0%	59.3%
5022395	101.1.2.19 ↗	alpha arrays › HTH › HTH › winged helix domain › Topoisom_bac	0.88	52.0	5.37e-01	100.0%	61.8%
5008813	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.87	50.0	5.11e-01	100.0%	59.4%
4976528	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.85	52.0	4.97e-01	100.0%	55.3%
5041057	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.75	39.0	5.15e-01	91.2%	89.5%
3614122	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.73	36.0	4.99e-01	92.9%	92.0%
5058268	101.1.2.54 ↗	alpha arrays › HTH › HTH › winged helix domain › Penicillinase_R	0.73	34.0	4.16e-01	87.6%	67.0%
4593646	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.73	39.0	5.36e-01	97.1%	100.0%
4974951	101.1.2.101 ↗	alpha arrays › HTH › HTH › winged helix domain › Cdc6_C	0.71	40.0	5.31e-01	98.2%	98.9%
4456203	101.1.2.19 ↗	alpha arrays › HTH › HTH › winged helix domain › Topoisom_bac	0.71	52.0	4.69e-01	100.0%	57.3%
4988184	101.1.2.101 ↗	alpha arrays › HTH › HTH › winged helix domain › Cdc6_C	0.71	38.0	5.18e-01	94.1%	98.9%
4524417	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.70	38.0	5.11e-01	98.8%	97.9%
3889516	101.1.2.206 ↗	alpha arrays › HTH › HTH › winged helix domain › SAMD1_WH	0.69	36.0	4.46e-01	87.6%	80.0%
3473498	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.67	33.0	4.62e-01	87.6%	95.3%
3718412	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.64	35.0	2.85e-01	90.6%	29.8%
5018748	101.1.2.100 ↗	alpha arrays › HTH › HTH › winged helix domain › FeoC	0.62	36.0	4.78e-01	88.2%	100.0%
5058376	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.61	35.0	4.46e-01	91.8%	98.9%
1807411	101.1.2.215 ↗	alpha arrays › HTH › HTH › winged helix domain › CmlS_C	0.54	29.0	3.36e-01	87.1%	70.6%
4309308	275.1.1.0 ↗	a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	0.50	18.0	2.53e-01	89.4%	61.3%

D3 medium residues 231-320_341-464

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01131.26 best	Topoisom_bac	135.8	3.00e-39	91.1%	42.5%

CATH (4)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1wznA02	2.20.25.110	Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases	0.65	17.0	3.41e-01	86.0%	85.7%
3n8bA00	3.10.450.700	Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, ›	0.64	18.0	3.12e-01	89.3%	70.7%
3bxoA02	2.20.130.10	Mainly Beta › Single Sheet › S-adenosyl-L-methionine-dependent methyltransferases › CAC2371-like domains	0.61	17.0	3.19e-01	86.4%	81.4%
1ue6D00	2.40.50.140	Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins	0.55	19.0	2.66e-01	95.3%	58.7%

ECOD (4)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4006756	101.1.2.19 ↗	alpha arrays › HTH › HTH › winged helix domain › Topoisom_bac	0.87	53.0	4.61e-01	93.9%	43.3%
4152544	264.2.1.0 ↗	beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain	0.68	29.0	3.59e-01	98.6%	60.7%
3248736	295.1.1.4 ↗	a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › COMM_domain	0.56	18.0	2.91e-01	89.3%	71.2%
2780879	1172.1.1.1 ↗	beta barrels › UL131A-like › UL130 C-terminal domain › UL130 C-terminal domain › Gp_UL130	0.52	19.0	2.52e-01	79.9%	55.9%

D4 medium residues 605-694

PDB

Domain cluster: representative

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1yuaA01	3.30.65.10	Alpha Beta › 2-Layer Sandwich › Bacterial Topoisomerase I; domain 1 › Bacterial Topoisomerase I, domain 1	0.55	33.0	3.82e-01	94.4%	84.4%
1iv8A02	3.30.1590.10	Alpha Beta › 2-Layer Sandwich › Maltooligosyl trehalose synthase, domain 2 › Maltooligosyl trehalose synthase, domain 2	0.50	36.0	3.34e-01	96.7%	56.8%

ECOD (4)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3965661	375.1.1.9 ↗	few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-C4_Topoisom	0.53	31.0	3.76e-01	88.9%	94.5%
3576662	5.1.4.0 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed	0.51	38.0	2.71e-01	80.0%	38.6%
3436173	219.1.1.0 ↗	a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases	0.51	39.0	2.74e-01	84.4%	85.9%
4948212	2.1.1.0 ↗	beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein	0.51	28.0	3.00e-01	76.7%	61.3%

D5 medium residues 695-777

PDB

Domain cluster: representative

CATH (11)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2htaA00	2.70.98.10	Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 ›	0.63	44.0	2.95e-01	72.3%	45.1%
7obmA01	2.130.10.120	Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Prolyl oligopeptidase, N-terminal domain	0.60	43.0	2.96e-01	77.1%	32.4%
2z3zA01	2.140.10.30	Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Dipeptidylpeptidase IV, N-terminal domain	0.59	46.0	3.03e-01	86.7%	35.6%
2lydA00	2.30.29.30	Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)	0.56	41.0	3.50e-01	75.9%	73.1%
3oe3C00	2.40.128.200	Mainly Beta › Beta Barrel › Lipocalin › C-type lysozyme inhibitor	0.56	39.0	3.86e-01	73.5%	90.9%
6j9eJ00	3.30.160.560	Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain ›	0.55	38.0	4.14e-01	73.5%	90.9%
5cxmA00	2.102.10.10	Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain	0.54	38.0	3.60e-01	73.5%	68.7%
1ln1A00	3.30.530.20	Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain	0.52	38.0	2.88e-01	75.9%	87.7%
1cmxA00	3.40.532.10	Alpha Beta › 3-Layer(aba) Sandwich › Ubiquitin C-terminal Hydrolase UCH-l3 › Peptidase C12, ubiquitin carboxyl-terminal hydrolase	0.52	36.0	2.75e-01	73.5%	81.3%
6jhpA01	2.70.98.60	Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › alpha-galactosidase from lactobacil brevis	0.51	36.0	2.58e-01	74.7%	85.9%
4wy5A00	3.40.50.1820	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain	0.50	39.0	2.71e-01	86.7%	92.2%

ECOD (21)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4997139	223.2.1.0 ↗	a+b three layers › Profilin-like › profilin-like › profilin-like	0.67	41.0	3.46e-01	72.3%	37.0%
4182769	375.13.1.1 ↗	few secondary structure elements › Rubredoxin-like › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Toprim_C_rpt	0.67	46.0	5.30e-01	71.1%	100.0%
3315072	375.13.1.1 ↗	few secondary structure elements › Rubredoxin-like › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Toprim_C_rpt	0.64	45.0	4.94e-01	72.3%	98.5%
3474747	5.1.5.4 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › DPPIV_N	0.64	49.0	3.07e-01	83.1%	35.3%
163179	12.3.1.3 ↗	beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Aldose_epim	0.63	44.0	2.95e-01	72.3%	45.1%
3996007	5.1.5.4 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › DPPIV_N	0.63	47.0	2.95e-01	79.5%	35.7%
3840141	331.1.1.5 ↗	a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › OGG_N	0.62	36.0	3.65e-01	74.7%	57.5%
4027836	220.1.1.13 ↗	beta barrels › PH domain-like › PH domain-like › PH domain-like › DCP1	0.62	44.0	3.58e-01	73.5%	59.3%
3937216	220.1.1.13 ↗	beta barrels › PH domain-like › PH domain-like › PH domain-like › DCP1	0.61	44.0	3.80e-01	75.9%	73.1%
3212508	5.1.4.32 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Nucleoporin_N	0.59	46.0	2.92e-01	85.5%	52.2%
3336598	206.1.1.1 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase	0.59	41.0	2.90e-01	73.5%	42.3%
3257727	216.1.1.0 ↗	a+b two layers › UBC-like › UBC-like › UBC-like	0.59	45.0	3.93e-01	83.1%	75.4%
3268906	5.1.10.0 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 12-bladed	0.57	40.0	3.92e-01	73.5%	83.1%
3717723	223.2.1.0 ↗	a+b three layers › Profilin-like › profilin-like › profilin-like	0.56	40.0	3.83e-01	77.1%	78.0%
3809935	5.1.5.0 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed	0.55	46.0	3.03e-01	95.2%	30.9%
4024830	5.1.4.0 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed	0.54	39.0	2.81e-01	77.1%	30.7%
3740262	220.1.1.0 ↗	beta barrels › PH domain-like › PH domain-like › PH domain-like	0.53	38.0	3.33e-01	74.7%	72.3%
3489862	5.1.5.0 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed	0.52	44.0	2.64e-01	100.0%	36.2%
3233686	220.1.1.13 ↗	beta barrels › PH domain-like › PH domain-like › PH domain-like › DCP1	0.52	41.0	3.54e-01	89.2%	75.2%
3598462	220.1.1.0 ↗	beta barrels › PH domain-like › PH domain-like › PH domain-like	0.52	37.0	3.35e-01	77.1%	70.4%
5051613	223.2.1.0 ↗	a+b three layers › Profilin-like › profilin-like › profilin-like	0.51	36.0	3.28e-01	74.7%	99.2%