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DNA_polymerase

Euk-Vir

Human_mastadenovirus_B

DNA_polymerase__YP_002213831__Human_mastadenovirus_B__108098

Identity

Accession:: YP_002213831 ↗
Protein ID:: DNA_polymerase
Kingdom:: euk

Quality

71.7 mean pLDDT

Taxonomy

Bamfordvirae› Preplasmiviricota› Pharingeaviricetes› Rowavirales› Adenoviridae› Mastadenovirus› Human_mastadenovirus_B

TaxID: 108098

Cluster

View cluster (24 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 97-179_199-232

PDB

Domain cluster: rep: DNA_polymerase__YP_009246380__Bat_mastadenovirus_WIV10__1788432__D69-178

CATH (5)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
7pl7A01	3.90.70.80	Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A ›	0.62	50.0	4.64e-01	88.0%	97.4%
4bouA00	3.90.70.80	Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A ›	0.62	51.0	4.80e-01	88.9%	95.7%
4bopB00	3.90.70.80	Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A ›	0.61	49.0	4.57e-01	88.0%	96.0%
6dx5A00	3.90.70.80	Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A ›	0.60	47.0	4.18e-01	83.8%	90.5%
4boqA00	3.90.70.80	Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A ›	0.57	46.0	4.01e-01	86.3%	91.4%

ECOD (8)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3421427	219.1.1.48 ↗	a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C65	0.64	52.0	4.11e-01	88.0%	95.9%
3786918	219.1.1.15 ↗	a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › OTU	0.62	50.0	4.53e-01	88.0%	98.2%
3763030	219.1.1.15 ↗	a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › OTU	0.62	51.0	4.24e-01	89.7%	67.3%
3356938	219.1.1.15 ↗	a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › OTU	0.61	51.0	4.65e-01	89.7%	89.0%
3993036	219.1.1.15 ↗	a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › OTU	0.60	50.0	4.82e-01	89.7%	98.5%
3512135	239.1.1.6 ↗	beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › tRNA-synt_1c_C2	0.60	24.0	2.72e-01	94.0%	44.4%
3743318	2006.1.1.0 ↗	a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like	0.56	38.0	3.16e-01	70.1%	63.8%
4953151	3111.1.1.0 ↗	beta barrels › STT3/PglB/AglB beta-barrel domain › STT3/PglB/AglB beta-barrel domain › STT3/PglB/AglB beta-barrel domain	0.52	37.0	3.78e-01	73.5%	97.4%

D2 medium residues 339-408_426-491

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03175.19 best	DNA_pol_B_2	32.0	9.00e-08	39.0%	12.4%

CATH (7)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2qkdA01	2.20.25.420	Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ZPR1, zinc finger domain	0.67	23.0	3.75e-01	89.0%	85.4%
2kpnA01	2.60.40.10	Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins	0.55	27.0	3.39e-01	98.5%	77.9%
2khxA00	3.30.160.20	Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain ›	0.55	26.0	3.23e-01	91.2%	70.9%
6xrbA01	3.40.1000.10	Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich	0.54	29.0	2.91e-01	93.4%	47.5%
1cp9B02	2.30.120.10	Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region	0.52	25.0	3.26e-01	83.8%	82.2%
1fm2B03	2.30.120.10	Mainly Beta › Roll › Penicillin G acylase, beta-roll domain › Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region	0.51	22.0	2.88e-01	86.8%	72.7%
1kiaA01	3.30.46.10	Alpha Beta › 2-Layer Sandwich › Glycine N-methyltransferase; chain A, domain 1 › Glycine N-methyltransferase, chain A, domain 1	0.51	28.0	3.48e-01	87.5%	88.0%

D3 medium residues 647-666_688-846_965-977

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03175.19 best	DNA_pol_B_2	204.2	5.40e-60	97.9%	41.2%

CATH (11)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2oo2A00	1.20.1270.90	Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like	0.72	23.0	3.75e-01	88.5%	73.7%
4u1cA01	4.10.860.10	Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain	0.70	19.0	4.01e-01	83.9%	92.3%
4b6xA00	1.20.58.90	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.70	21.0	3.70e-01	82.3%	78.3%
2v6yA00	1.20.58.80	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit	0.69	22.0	3.59e-01	85.4%	73.3%
1luwA01	1.10.287.990	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain	0.65	22.0	3.83e-01	84.4%	90.6%
6he1B01	1.10.287.40	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain	0.64	23.0	4.06e-01	88.5%	100.0%
4rngC00	1.20.1280.290	Mainly Alpha › Up-down Bundle › Monooxygenase ›	0.60	20.0	3.13e-01	96.9%	69.9%
3craB01	1.10.287.1080	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like	0.60	22.0	3.43e-01	94.8%	79.1%
1vmgA00	1.10.287.1080	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like	0.55	22.0	3.48e-01	94.8%	90.2%
1yvwA00	1.10.287.1080	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like	0.54	22.0	3.26e-01	96.9%	81.5%
2yfaA02	1.20.1440.210	Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) ›	0.53	27.0	3.38e-01	89.6%	78.4%

ECOD (12)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4651639	2484.1.1.36 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2	0.80	77.0	6.05e-01	100.0%	56.1%
5025189	192.17.1.0 ↗	alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like	0.78	21.0	4.34e-01	83.3%	89.1%
3889863	277.1.1.1 ↗	a+b two layers › PX domain › PX domain › PX domain › PX	0.77	27.0	3.51e-01	89.6%	54.2%
3721261	192.3.1.1 ↗	alpha bundles › Long alpha-hairpin › Fe,Mn superoxide dismutase (SOD), N-terminal domain › Fe,Mn superoxide dismutase (SOD), N-terminal domain › Sod_Fe_N	0.66	21.0	3.89e-01	84.4%	91.7%
3965106	605.1.1.4 ↗	alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3	0.66	23.0	3.78e-01	78.1%	82.7%
3227443	375.10.1.2 ↗	few secondary structure elements › Rubredoxin-like › Zinc finger domain of DNA polymerase-alpha › Zinc finger domain of DNA polymerase-alpha › zf-DPOE	0.63	17.0	3.15e-01	73.4%	75.0%
4400977	604.34.1.0 ↗	alpha bundles › Spectrin repeat-like › Helical bundle domain in arginine decarboxylase › Helical bundle domain in arginine decarboxylase	0.63	23.0	3.52e-01	90.6%	76.5%
3186698	192.17.1.0 ↗	alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like	0.60	24.0	3.61e-01	96.4%	85.0%
4477580	5086.1.1.118 ↗	alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › BBS2_hp	0.59	23.0	3.41e-01	81.8%	78.8%
3968795	304.48.1.3 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B	0.57	40.0	3.55e-01	100.0%	50.4%
3738041	192.5.1.1 ↗	alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1	0.57	24.0	3.45e-01	98.4%	84.7%
3576407	622.4.1.0 ↗	alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related	0.53	26.0	3.27e-01	99.0%	76.5%

D4 medium residues 667-687_978-1193

PDB

Domain cluster: rep: KY817360.1__ARK07690.1__Toil_gp07__00007__D228-251_428-596

CATH (6)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2qyxB01	3.30.70.1360	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › mj0159-like	0.63	25.0	3.61e-01	91.1%	77.1%
1m1hA01	3.30.70.940	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › NusG, N-terminal domain	0.59	27.0	3.90e-01	81.0%	96.0%
3ui3A02	3.30.70.240	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits ›	0.55	25.0	3.71e-01	79.7%	100.0%
2gffA00	3.30.70.100	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits ›	0.55	23.0	3.65e-01	86.5%	99.0%
3gqcC01	3.30.70.270	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain	0.51	29.0	3.75e-01	89.0%	97.1%
1iujA00	3.30.70.100	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits ›	0.50	24.0	3.45e-01	87.3%	100.0%

ECOD (6)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4651639	2484.1.1.36 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2	0.64	53.0	4.54e-01	85.7%	88.9%
5177	304.4.1.0 ↗	a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel	0.58	26.0	3.96e-01	89.0%	100.0%
4980062	304.4.1.0 ↗	a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel	0.56	25.0	3.73e-01	83.5%	98.9%
5029117	304.4.1.0 ↗	a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel	0.56	26.0	3.76e-01	81.4%	94.5%
4026407	304.4.1.0 ↗	a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel	0.51	26.0	3.45e-01	83.1%	87.7%
4024206	304.9.1.0 ↗	a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD	0.51	25.0	3.44e-01	76.8%	94.5%