←Back to structures

NC_070937.1__YP_010665926.1__PQB73_gp098__00208

Bact-Vir

Identity

Accession:: NC_070937 ↗
Kingdom:: phage

Quality

90.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Straboviridae› Nanhuvirus› Cronobacter_phage_LPCS28

TaxID: 2924885

Cluster

View cluster (10 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 2-91

PDB

Domain cluster: rep: peptidyl-tRNA_hydrolase__YP_009447948__Flamingopox_virus_FGPVKD09__2059380__D17-122

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01981.22 best	PTH2	24.3	4.20e-05	90.0%	67.0%

CATH (7)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1nbeB01	3.30.70.140	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Aspartate carbamoyltransferase regulatory subunit, N-terminal domain	0.57	32.0	3.19e-01	100.0%	51.6%
5cvdB00	3.40.50.150	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39	0.54	42.0	3.28e-01	87.8%	80.5%
3e6qA00	3.30.429.10	Alpha Beta › 2-Layer Sandwich › Macrophage Migration Inhibitory Factor › Macrophage Migration Inhibitory Factor	0.52	46.0	4.16e-01	100.0%	84.1%
8gjaD01	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.51	37.0	2.77e-01	78.9%	61.9%
3jv9A01	3.40.190.10	Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II	0.51	42.0	4.00e-01	93.3%	97.2%
3fd3A01	3.40.190.10	Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II	0.51	42.0	3.98e-01	100.0%	77.4%
1nvmB02	3.30.360.10	Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2	0.50	42.0	3.66e-01	98.9%	94.8%

ECOD (14)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4559979	2501.1.1.1 ↗	a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › PTH2	0.88	83.0	7.43e-01	100.0%	81.7%
3599010	2501.1.1.0 ↗	a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II	0.88	82.0	7.11e-01	98.9%	86.9%
4946237	2501.1.1.1 ↗	a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › PTH2	0.87	81.0	7.41e-01	100.0%	83.5%
3354413	2501.1.1.1 ↗	a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › PTH2	0.87	82.0	7.34e-01	100.0%	79.8%
3280180	2501.1.1.0 ↗	a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II	0.87	67.0	6.94e-01	84.4%	85.9%
5030351	2501.1.1.1 ↗	a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › PTH2	0.87	81.0	7.37e-01	100.0%	82.6%
3628884	2501.1.1.1 ↗	a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › PTH2	0.84	79.0	7.21e-01	100.0%	82.3%
3277850	2501.1.1.1 ↗	a/b three-layered sandwiches › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › Peptidyl-tRNA hydrolase II › PTH2	0.79	73.0	7.20e-01	100.0%	94.7%
3304252	320.1.1.3 ↗	a+b two layers › R3H domain-like › R3H domain › R3H domain › YlmH_1st	0.74	38.0	4.24e-01	100.0%	62.9%
3824796	320.1.1.0 ↗	a+b two layers › R3H domain-like › R3H domain › R3H domain	0.66	35.0	3.97e-01	100.0%	66.7%
4139696	2003.1.5.46 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › MTS	0.53	42.0	3.30e-01	88.9%	91.2%
3292011	2003.1.5.154 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_29, Methyltransf_11	0.52	40.0	2.62e-01	87.8%	34.2%
3284267	7523.1.1.15 ↗	a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › LysR_substrate	0.52	42.0	3.24e-01	90.0%	99.0%
4651438	2003.1.5.46 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › MTS	0.51	42.0	3.29e-01	92.2%	90.7%

D2 medium residues 106-163

PDB

Domain cluster: representative

CATH (9)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3o8sA00	3.90.79.10	Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase	0.61	52.0	4.03e-01	98.3%	70.9%
4gvbB00	3.30.70.440	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Killer toxin KP6 alpha-subunit	0.57	43.0	4.04e-01	84.5%	90.5%
3oymA01	1.10.340.70	Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 ›	0.57	40.0	3.46e-01	74.1%	69.9%
5zx8A00	3.40.50.1470	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidyl-tRNA hydrolase	0.56	44.0	3.23e-01	93.1%	88.2%
2jrjA00	3.30.40.10	Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger)	0.53	32.0	3.38e-01	98.3%	65.4%
3nrfA00	2.60.40.4110	Mainly Beta › Sandwich › Immunoglobulin-like › Protein of unknown function DUF4354	0.52	40.0	3.36e-01	84.5%	56.9%
2m8cA01	3.40.190.10	Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II	0.51	36.0	2.82e-01	75.9%	35.0%
5u3fB01	3.30.470.10	Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain	0.50	35.0	2.80e-01	77.6%	55.7%
4kxfL01	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.50	38.0	2.67e-01	84.5%	79.3%

ECOD (16)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4981250	304.128.1.0 ↗	a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB	0.67	50.0	4.30e-01	82.8%	89.5%
3504415	221.4.1.1 ↗	a+b two layers › beta-Grasp › Nudix › Nudix › NUDIX	0.63	51.0	3.93e-01	93.1%	70.5%
4547125	375.14.1.0 ↗	few secondary structure elements › Rubredoxin-like › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1) › Rubredoxin-like domain in leucyl-tRNA synthetase (LS1)	0.62	39.0	4.17e-01	94.8%	76.0%
3781211	101.1.1.0 ↗	alpha arrays › HTH › HTH › Three-helical HTH	0.61	42.0	3.55e-01	74.1%	83.8%
3696515	2003.1.5.81 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25	0.59	44.0	2.87e-01	82.8%	51.2%
4245376	3933.1.1.1 ↗	a+b two layers › Uncharacterized protein YPO2434 › Uncharacterized protein YPO2434 › Uncharacterized protein YPO2434 › KTSC	0.58	46.0	4.64e-01	94.8%	91.7%
2096143	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.57	35.0	3.17e-01	93.1%	41.8%
4966636	206.1.3.0 ↗	a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp	0.57	49.0	3.33e-01	96.6%	42.4%
3927186	101.1.1.76 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Integrase_H2C2	0.57	38.0	3.39e-01	70.7%	81.1%
4495413	2.8.1.0 ↗	beta barrels › OB-fold › mu transposases-C › mu transposases-C	0.57	44.0	4.24e-01	96.6%	74.3%
3581513	4357.1.1.1 ↗	beta barrels › WWE domain › WWE domain › WWE domain › WWE	0.55	46.0	4.16e-01	94.8%	81.2%
3254632	4357.1.1.1 ↗	beta barrels › WWE domain › WWE domain › WWE domain › WWE	0.55	44.0	4.31e-01	93.1%	96.9%
4960570	10.1.1.0 ↗	beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases	0.52	41.0	2.74e-01	87.9%	27.6%
3206098	577.1.1.1 ↗	alpha arrays › CRIB domain › CRIB domain › CRIB domain › PBD	0.52	38.0	3.84e-01	81.0%	78.3%
3953844	304.24.1.34 ↗	a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › DUF3145	0.52	38.0	2.98e-01	84.5%	95.2%
3920678	5.1.5.41 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40_2	0.51	37.0	2.33e-01	79.3%	97.2%