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S2_012_000_R2_scaffold_0_prodigal-single.1__X__X__00896

Bact-Vir

S2_012_000_R2_scaffold_0_prodigal-single.1__X__X__00896

Identity

Kingdom:
phage

Quality

87.7 mean pLDDT

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 high residues 58-134
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01471.24 best PG_binding_1 38.3 1.70e-09 76.6% 89.5%
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3bkhA01 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.90 80.0 7.65e-01 94.8% 82.6%
4g54A02 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.90 76.0 7.91e-01 97.4% 95.8%
4c2dA02 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.89 82.0 7.89e-01 100.0% 88.2%
1lbuA01 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.83 74.0 7.23e-01 98.7% 88.1%
7aj9A01 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.82 61.0 6.48e-01 79.2% 89.6%
1eakA01 1.10.101.10 Mainly Alpha › Orthogonal Bundle › Muramoyl-pentapeptide Carboxypeptidase; domain 1 › PGBD-like superfamily/PGBD 0.80 55.0 6.07e-01 96.1% 87.3%
1ck7A01 3.40.390.10 Alpha Beta › 3-Layer(aba) Sandwich › Collagenase (Catalytic Domain) › Collagenase (Catalytic Domain) 0.80 54.0 3.78e-01 92.2% 23.0%
2ckoA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.54 40.0 2.80e-01 79.2% 94.4%
4hjhA03 3.40.120.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 › Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 0.54 44.0 3.90e-01 90.9% 99.1%
2nr7A00 1.20.141.10 Mainly Alpha › Up-down Bundle › Chitosanase, subunit A; domain 1 › Chitosanase, subunit A, domain 1 0.54 48.0 3.58e-01 100.0% 65.5%
2r2iA02 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.51 42.0 4.14e-01 98.7% 85.1%
ECOD (64)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2859574 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.94 74.0 7.71e-01 90.9% 88.7%
4117418 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.93 66.0 7.50e-01 77.9% 93.3%
3955223 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.93 80.0 7.95e-01 89.6% 93.8%
1498420 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.93 76.0 7.72e-01 92.2% 86.8%
1165079 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.92 83.0 7.59e-01 100.0% 76.0%
3957237 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.91 77.0 7.89e-01 88.3% 98.7%
4218606 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.91 78.0 7.58e-01 93.5% 83.1%
224034 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.90 76.0 7.46e-01 96.1% 84.0%
4173379 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.90 80.0 7.95e-01 94.8% 90.0%
4032027 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.89 83.0 7.99e-01 100.0% 88.2%
4312892 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.89 64.0 7.20e-01 80.5% 95.0%
3356981 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.88 76.0 7.53e-01 92.2% 87.5%
3959835 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.87 75.0 7.92e-01 90.9% 100.0%
4473649 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.87 82.0 7.92e-01 100.0% 95.3%
3946056 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.87 71.0 6.27e-01 100.0% 62.0%
4380775 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.86 63.0 4.49e-01 81.8% 29.0%
3275963 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 81.0 7.64e-01 100.0% 95.6%
3291401 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 79.0 7.59e-01 97.4% 87.1%
3299326 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 63.0 6.87e-01 80.5% 90.8%
3589440 144.1.1.7 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PF30262 0.86 81.0 6.45e-01 100.0% 71.4%
4096813 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 81.0 7.33e-01 100.0% 96.0%
3319740 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.86 78.0 7.52e-01 97.4% 89.4%
1934000 144.1.1.2 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1,PG_binding_5 0.86 81.0 6.21e-01 100.0% 56.3%
5019285 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.85 80.0 7.39e-01 100.0% 88.4%
3263339 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.85 73.0 7.40e-01 90.9% 94.7%
1877329 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.84 65.0 6.56e-01 90.9% 81.6%
4055540 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.84 63.0 6.62e-01 90.9% 87.0%
4010440 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.84 71.0 7.26e-01 96.1% 93.3%
3299934 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.83 77.0 6.89e-01 100.0% 81.9%
3395 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.83 74.0 7.27e-01 98.7% 89.2%
4011396 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.82 77.0 6.62e-01 100.0% 84.1%
3302194 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.82 75.0 6.96e-01 100.0% 89.5%
2819638 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.82 75.0 6.48e-01 100.0% 66.4%
3332533 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.82 75.0 6.82e-01 98.7% 91.0%
3772398 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.82 64.0 6.32e-01 88.3% 78.8%
3539881 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.80 62.0 6.33e-01 93.5% 84.0%
3893524 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.80 59.0 6.24e-01 77.9% 85.7%
4600634 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.79 58.0 6.45e-01 77.9% 98.3%
3060287 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.79 61.0 6.22e-01 90.9% 84.0%
3994858 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.79 60.0 6.00e-01 97.4% 77.5%
4160453 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.78 58.0 6.06e-01 100.0% 85.7%
3930763 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.77 62.0 6.28e-01 92.2% 86.7%
3765966 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.77 60.0 5.79e-01 93.5% 74.1%
1904136 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.77 61.0 6.18e-01 87.0% 85.3%
3537259 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.77 61.0 6.06e-01 93.5% 81.2%
4997479 144.1.1.11 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_2 0.76 64.0 6.19e-01 90.9% 83.5%
3764906 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.75 59.0 5.88e-01 93.5% 80.0%
3933825 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.75 59.0 6.06e-01 97.4% 86.7%
3631772 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.75 64.0 4.75e-01 90.9% 61.1%
3221065 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.75 63.0 6.42e-01 93.5% 92.0%
3788528 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.74 63.0 4.93e-01 90.9% 73.5%
3772718 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.74 58.0 5.65e-01 98.7% 75.3%
4962391 144.1.1.11 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_2 0.73 61.0 5.74e-01 87.0% 80.0%
3247155 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.73 52.0 5.62e-01 90.9% 89.2%
4945529 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.72 57.0 6.11e-01 89.6% 100.0%
4857662 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.71 51.0 5.37e-01 98.7% 83.1%
3222017 144.1.1.0 alpha arrays › PGBD-like › PGBD-like › PGBD-like 0.69 59.0 5.64e-01 92.2% 81.1%
3621525 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.67 57.0 5.78e-01 96.1% 93.3%
4262263 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.66 53.0 5.35e-01 88.3% 89.3%
3274761 144.1.1.1 alpha arrays › PGBD-like › PGBD-like › PGBD-like › PG_binding_1 0.65 55.0 4.24e-01 90.9% 67.9%
1933281 4126.1.1.3 a/b three-layered sandwiches › beta-carbonic anhydrase-like › beta-carbonic anhydrase › beta-carbonic anhydrase › LCIB_C_CA 0.59 43.0 3.15e-01 77.9% 66.2%
7431 235.1.1.13 a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glyco_hydro_108,PG_binding_3 0.54 48.0 3.59e-01 100.0% 66.1%
3225299 5054.1.1.1 alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Lig_chan 0.52 35.0 2.93e-01 71.4% 39.3%
5044527 169.1.1.1 alpha complex topology › Aldehyde ferredoxin oxidoreductase-C › Aldehyde ferredoxin oxidoreductase-C › Aldehyde ferredoxin oxidoreductase-C › AFOR_C 0.51 43.0 2.80e-01 100.0% 26.0%
D2 high residues 163-339
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03734.20 best YkuD 70.9 2.40e-19 85.3% 95.9%
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zatA02 2.40.440.10 Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.87 60.0 7.18e-01 87.0% 100.0%
2mtzA02 2.40.440.10 Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.86 54.0 6.59e-01 88.7% 94.1%
3tx4A02 2.40.440.10 Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.83 61.0 6.82e-01 98.3% 93.0%
4z7aA03 2.40.440.10 Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.81 55.0 6.35e-01 98.3% 91.6%
4lpqA02 2.40.440.10 Mainly Beta › Beta Barrel › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.80 55.0 6.41e-01 87.0% 95.3%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4679621 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.90 66.0 7.62e-01 87.0% 98.5%
3163824 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.89 87.0 7.22e-01 100.0% 80.4%
3968640 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.88 56.0 6.74e-01 88.1% 91.2%
2819641 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.88 86.0 7.72e-01 100.0% 96.9%
3974213 4091.1.1.0 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.87 68.0 7.56e-01 89.3% 97.2%
4302389 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.87 64.0 7.27e-01 91.0% 95.7%
3964337 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.86 77.0 7.26e-01 100.0% 79.8%
3957156 4091.1.1.0 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like 0.86 54.0 6.29e-01 97.2% 86.2%
None 0.85 68.0 7.38e-01 93.2% 96.0%
1220824 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.83 61.0 6.19e-01 98.3% 75.9%
997880 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.82 57.0 6.70e-01 87.0% 96.9%
1498421 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.80 51.0 5.63e-01 87.0% 78.6%
4410211 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.76 54.0 6.31e-01 87.0% 99.2%
3951628 4091.1.1.1 beta complex topology › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › L,D-transpeptidase catalytic domain-like › YkuD 0.75 60.0 6.55e-01 87.0% 96.7%
3981189 3743.1.1.0 a+b two layers › L,D-transpeptidase C-terminal domain › L,D-transpeptidase C-terminal domain › L,D-transpeptidase C-terminal domain 0.75 73.0 6.59e-01 100.0% 78.7%
4634740 2484.1.1.136 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MutL 0.57 31.0 3.95e-01 100.0% 86.4%
3351082 5.1.5.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40 0.57 27.0 2.75e-01 82.5% 43.9%
4995200 3407.1.1.2 mixed a+b and a/b › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Nop5_56-rel_N_Arc 0.54 33.0 3.98e-01 98.3% 93.0%
4072881 304.12.1.0 a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 0.51 22.0 3.21e-01 76.8% 87.5%