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VP1

Euk-Vir

Thetapolyomavirus_trebernacchii

VP1__YP_009552744__Thetapolyomavirus_trebernacchii__2218588

Identity

Accession:
YP_009552744 ↗
Protein ID:
VP1
Kingdom:
euk

Quality

65.0 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 4-224
PDB
Domain cluster: rep: VP1__YP_009325930__Betapolyomavirus_securanorvegicus__1919247__D30-309
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00718.29 best Polyoma_coat 42.3 6.80e-11 47.5% 34.5%
CATH (57)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3s7vC00 2.60.175.10 Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus 0.86 82.0 7.57e-01 98.2% 99.6%
1sidF00 2.60.175.10 Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus 0.85 78.0 6.43e-01 94.1% 81.9%
4oi4C01 2.60.120.1030 Mainly Beta › Sandwich › Jelly Rolls › Clp1, DNA binding domain 0.67 25.0 3.88e-01 91.4% 84.5%
1o6uA02 2.60.120.680 Mainly Beta › Sandwich › Jelly Rolls › GOLD domain 0.66 33.0 4.63e-01 88.7% 98.1%
1dzlA00 2.60.175.20 Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Major capsid L1 (late) superfamily, Papillomavirus 0.66 62.0 4.81e-01 100.0% 80.4%
1yi9A01 2.60.120.310 Mainly Beta › Sandwich › Jelly Rolls › Copper type II, ascorbate-dependent monooxygenase, N-terminal domain 0.65 43.0 5.03e-01 93.7% 92.9%
5u55A02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.65 29.0 3.78e-01 91.9% 72.1%
4lr4A02 2.60.120.1430 Mainly Beta › Sandwich › Jelly Rolls › 0.65 44.0 5.01e-01 97.7% 90.5%
3g7dA03 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.63 31.0 4.04e-01 93.7% 82.3%
1blwA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 27.0 3.82e-01 95.5% 83.3%
1fnfA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 25.0 3.73e-01 94.1% 85.1%
1fnfA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 25.0 3.68e-01 91.0% 85.4%
2v5yA05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 25.0 3.62e-01 89.6% 80.4%
2pn5A07 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 29.0 3.94e-01 91.0% 87.7%
2hevF00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.61 35.0 4.56e-01 92.3% 98.4%
2xbzA00 2.60.40.2380 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 28.0 3.55e-01 89.1% 72.0%
3l5iA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 23.0 3.49e-01 89.1% 83.0%
1va9A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 29.0 3.82e-01 99.1% 82.8%
3bb6C00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.59 29.0 3.91e-01 99.1% 89.3%
4gioA00 2.60.40.3230 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 26.0 3.83e-01 93.2% 93.8%
1opoC01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.58 42.0 4.75e-01 93.7% 97.6%
1ollA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 25.0 3.50e-01 91.4% 84.2%
7y8sA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 24.0 3.50e-01 89.1% 85.3%
4zxeC00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.57 35.0 4.39e-01 92.8% 98.5%
6xaxA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 22.0 3.36e-01 90.5% 84.7%
8ehtB01 2.60.40.1090 Mainly Beta › Sandwich › Immunoglobulin-like › Fimbrial-type adhesion domain 0.57 38.0 4.53e-01 91.0% 100.0%
1auyB00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.57 42.0 4.47e-01 98.2% 87.8%
2ztnA01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.56 44.0 4.73e-01 94.6% 95.8%
3eb7A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 36.0 4.15e-01 91.0% 89.0%
2zgoA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.55 39.0 4.45e-01 91.0% 95.2%
1wcuA00 2.60.120.430 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding lectin 0.55 34.0 4.12e-01 91.9% 92.6%
1gwmA00 2.60.120.430 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding lectin 0.55 34.0 4.01e-01 94.6% 88.9%
5axgA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 25.0 3.25e-01 89.6% 75.4%
3m70A01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.54 26.0 3.50e-01 92.3% 88.7%
4devD01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 31.0 3.95e-01 92.3% 98.4%
1tdqA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 25.0 3.61e-01 82.8% 100.0%
1o91A00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.53 32.0 4.05e-01 91.4% 100.0%
1mkfA01 2.60.40.1330 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 36.0 3.82e-01 94.1% 75.9%
1wfoA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 25.0 3.47e-01 83.7% 91.3%
4w8jA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.53 36.0 4.23e-01 93.7% 98.1%
4qc8A00 2.170.30.10 Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 0.52 46.0 3.55e-01 94.1% 86.9%
2pn5A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.52 25.0 3.52e-01 85.1% 99.0%
2g8gA00 2.170.30.10 Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 0.52 46.0 3.45e-01 94.6% 87.8%
1pgsA02 2.60.120.230 Mainly Beta › Sandwich › Jelly Rolls › 0.52 37.0 4.16e-01 95.0% 93.7%
3zx7A01 2.60.120.980 Mainly Beta › Sandwich › Jelly Rolls › 0.52 29.0 3.36e-01 78.7% 73.6%
1c8dA00 2.170.30.10 Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 0.51 45.0 3.41e-01 95.0% 96.9%
1uenA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 26.0 3.23e-01 70.1% 79.2%
3vmnA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 28.0 3.41e-01 86.0% 81.7%
1w3fA02 2.170.15.10 Mainly Beta › Beta Complex › Proaerolysin; Chain A, domain 3 › Proaerolysin, chain A, domain 3 0.51 31.0 3.56e-01 98.2% 80.0%
2re9A01 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.51 36.0 4.16e-01 91.0% 100.0%
1pmhX00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 40.0 4.38e-01 94.6% 98.9%
4d8mA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.50 34.0 3.80e-01 94.6% 87.1%
1s58A00 2.170.30.10 Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 0.50 44.0 3.36e-01 94.1% 86.4%
4p04A01 2.60.40.3100 Mainly Beta › Sandwich › Immunoglobulin-like › Arylsulphate sulphotransferase monomer, N-terminal domain 0.50 24.0 3.31e-01 86.0% 90.6%
5j7mA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.50 26.0 3.32e-01 82.8% 86.1%
3u4kA00 2.60.40.3310 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 32.0 3.67e-01 91.9% 85.9%
1oq1B00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.50 43.0 4.38e-01 91.4% 98.2%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2666438 10.2.1.6 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat 0.85 78.0 6.55e-01 94.1% 81.2%
423236 10.2.1.6 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat 0.83 80.0 7.39e-01 99.1% 99.6%
961478 10.2.1.6 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat 0.82 72.0 6.82e-01 90.5% 100.0%
3865949 10.4.1.0 ↗ beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain 0.71 35.0 4.97e-01 93.2% 98.1%
4972682 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.68 33.0 4.63e-01 90.0% 96.2%
5040234 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.67 37.0 4.90e-01 93.7% 100.0%
3892939 10.32.1.229 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › PF27640 0.67 37.0 4.51e-01 90.5% 82.9%
1111986 10.32.1.84 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › DUF6947 0.66 43.0 5.10e-01 93.7% 95.9%
3246388 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.65 34.0 4.38e-01 95.5% 89.9%
3714436 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.64 36.0 4.64e-01 91.9% 93.1%
4245506 11.1.1.6 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › A2M 0.64 29.0 4.03e-01 91.0% 85.7%
3519988 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.64 32.0 4.42e-01 91.0% 95.5%
3937082 10.4.1.0 ↗ beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain 0.64 34.0 4.49e-01 92.8% 96.5%
3528787 11.1.1.6 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › A2M 0.64 30.0 3.93e-01 91.4% 79.2%
3558696 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 25.0 3.67e-01 96.4% 81.0%
4165675 10.12.1.118 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › PF30252 0.61 31.0 3.83e-01 94.1% 75.0%
3522661 10.21.1.1 ↗ beta sandwiches › jelly-roll › Jelly-roll domain in ADAMTS13 › Jelly-roll domain in ADAMTS13 › ADAMTS_spacer1 0.61 37.0 4.61e-01 95.0% 97.8%
3476169 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.61 31.0 4.04e-01 91.4% 87.5%
3692007 10.32.1.3 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Calpain_III 0.61 38.0 4.52e-01 89.6% 93.1%
5046043 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.60 36.0 4.57e-01 88.2% 97.0%
3909622 10.21.1.1 ↗ beta sandwiches › jelly-roll › Jelly-roll domain in ADAMTS13 › Jelly-roll domain in ADAMTS13 › ADAMTS_spacer1 0.60 36.0 4.42e-01 94.6% 93.6%
1877512 10.2.1.32 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Astro_capsid_N 0.59 46.0 5.01e-01 95.5% 98.4%
3919532 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.58 27.0 3.63e-01 92.8% 83.6%
3186200 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 23.0 3.48e-01 91.9% 90.6%
5038686 10.2.1.0 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.56 29.0 3.79e-01 91.4% 90.4%
3910912 11.1.1.3 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ig 0.56 27.0 3.66e-01 86.9% 88.2%
3597119 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.56 39.0 4.06e-01 91.9% 74.3%
4000176 10.7.1.0 ↗ beta sandwiches › jelly-roll › Hypothetical protein TM1070 › Hypothetical protein TM1070 0.56 25.0 3.38e-01 86.9% 81.9%
146646 10.2.1.30 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › SP2 0.55 44.0 4.65e-01 94.6% 94.8%
3922242 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.55 27.0 3.67e-01 87.3% 92.4%
3523734 11.1.1.3 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ig 0.55 28.0 3.67e-01 84.2% 88.2%
5040537 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 26.0 3.60e-01 91.4% 89.1%
1558581 4182.2.1.1 ↗ beta sandwiches › Agglutinin HPA-like › CofB C-terminal domain › CofB C-terminal domain › CofB_C 0.55 37.0 4.22e-01 97.3% 91.5%
3519065 11.1.1.842 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › CUT_C 0.54 31.0 3.84e-01 93.7% 89.6%
3668136 10.1.1.2 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Lectin_legB 0.54 46.0 4.33e-01 91.9% 98.9%
3717342 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.54 41.0 4.32e-01 92.3% 86.5%
4932923 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 26.0 3.40e-01 92.3% 82.6%
3919987 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 26.0 3.53e-01 87.8% 89.1%
5033659 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 27.0 3.65e-01 86.0% 94.5%
3524675 11.1.1.271 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_6 0.53 27.0 3.31e-01 86.4% 76.3%
164036 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.52 25.0 3.58e-01 85.1% 100.0%
3895304 10.32.1.6 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › P_proprotein 0.52 42.0 4.50e-01 100.0% 94.9%
2044957 10.2.1.1 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Rhv 0.52 44.0 4.22e-01 96.8% 78.4%
3648779 4111.1.1.2 ↗ a+b two layers › AF0104/ALDC/Ptd012-like › AF0104/ALDC/Ptd012-like › AF0104/ALDC/Ptd012-like › PCC 0.52 30.0 3.79e-01 96.4% 93.3%
5035707 4182.1.1.0 ↗ beta sandwiches › Agglutinin HPA-like › Agglutinin HPA-like › Agglutinin HPA-like 0.52 36.0 3.85e-01 94.1% 80.5%
178766 10.2.1.53 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › IHHNV_capsid 0.51 46.0 4.16e-01 96.4% 90.3%
3970201 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.51 39.0 4.28e-01 94.6% 97.2%
3844538 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.51 34.0 3.94e-01 88.2% 93.8%
3477334 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 30.0 3.79e-01 86.0% 100.0%
3398492 11.1.1.610 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_DSCAM-DSCAML_C 0.51 24.0 3.33e-01 83.7% 90.5%
3996699 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 28.0 3.68e-01 83.7% 97.5%
4498731 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.51 32.0 3.98e-01 90.0% 100.0%
3899215 11.1.1.850 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF28354 0.51 24.0 3.28e-01 84.6% 87.3%
3489233 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.51 43.0 4.30e-01 90.5% 97.8%
4242304 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.50 23.0 3.28e-01 87.3% 96.7%