LiteFold/DisProt huggingface dataset:
Protein: DP00485 (UniProt Q9UBE0)
Region: residues 178	to 203
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered regions not observed in electron density included Sae1 residues 178–203 and 346, and Sae2 residues 1–3, 219–237, 291–304, and 551–640.
Cross-references: PDB:1Y8Q
PDB:1Y8R
Protein: DP00485 (UniProt Q9UBE0)
Region: residues 1	to 24
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In SAE1, the N-terminal helices H1 and H2 that lie beneath the Cys domain and UBA2 helix 13 in the open conformation move out of the adenylation active site and become disordered in the closed conformation.
The authors referred as closed conformation the structure formed by the  E1~SUMO1-AVSN complex, whereas mention as open conformation the structure that forms the E1/SUMO1-AMSN complex.
Cross-references: PDB:3KYD
Protein: DP00485 (UniProt Q9UBE0)
Region: residues 9	to 24
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In SAE1, the N-terminal helices H1 and H2 that lie beneath the Cys domain and UBA2 helix 13 in the open conformation move out of the adenylation active site and become disordered in the closed conformation.
The authors referred as closed conformation the structure formed by the  E1~SUMO1-AVSN complex, whereas mention as open conformation the structure that forms the E1/SUMO1-AMSN complex.
Cross-references: PDB:3KYD
PDB:3KYC
Protein: DP00485 (UniProt Q9UBE0)
Region: residues 9	to 24
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In SAE1, the N-terminal helices H1 and H2 that lie beneath the Cys domain and UBA2 helix 13 in the open conformation move out of the adenylation active site and become disordered in the closed conformation.
The authors referred as closed conformation the structure formed by the  E1~SUMO1-AVSN complex, whereas mention as open conformation the structure that forms the E1/SUMO1-AMSN complex.
Cross-references: PDB:3KYC
Protein: DP00485 (UniProt Q9UBE0)
Region: residues 181	to 204
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contained SUMO1(19–97)-AMSN, SAE1 amino acids (aa) 9–180 and 205–345, and UBA2 aa 5–217, 235–291, 305–548 and 608–640. As full-length proteins were used in crystallization, residues not observed in electron density were presumed disordered.
Cross-references: PDB:3KYC
Protein: DP00485 (UniProt Q9UBE0)
Region: residues 184	to 203
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes SUMO1(20–97)-AVSN, SAE1 aa 25–183 and 204–345 and UBA2 aa 4–197, 240–290, 309–336 and 345–548. SUMO1(1–97)-AVSN, SAE1 and UBA2 (1–550) were crystallized, so residues not observed in electron density were presumed disordered.
Cross-references: PDB:3KYD
Protein: DP00485 (UniProt Q9UBE0)
Region: residues 270	to 294
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
The PDB data shows this region has high relative B-factor values, indicating it is disordered.
Cross-references: PDB:3KYC
Protein: DP00485 (UniProt Q9UBE0)
Region: residues 222	to 235
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
The PDB data shows this region has high relative B-factor values, indicating it is disordered.
Cross-references: PDB:3KYC
Protein: DP00485 (UniProt Q9UBE0)
Region: residues 176	to 208
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
The PDB data shows this region has high relative B-factor values, indicating it is disordered.
Cross-references: PDB:3KYC
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 291	to 304
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered regions not observed in electron density included Sae1 residues 178–203 and 346, and Sae2 residues 1–3, 219–237, 291–304, and 551–640.
Cross-references: PDB:1Y8Q
PDB:1Y8R
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 551	to 640
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered regions not observed in electron density included Sae1 residues 178–203 and 346, and Sae2 residues 1–3, 219–237, 291–304, and 551–640.
Cross-references: PDB:1Y8Q
PDB:1Y8R
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 219	to 237
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered regions not observed in electron density included Sae1 residues 178–203 and 346, and Sae2 residues 1–3, 219–237, 291–304, and 551–640.
Cross-references: PDB:1Y8Q
PDB:1Y8R
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 198	to 239
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model includes SUMO1(20–97)-AVSN, SAE1 aa 25–183 and 204–345 and UBA2 aa 4–197, 240–290, 309–336 and 345–548. SUMO1(1–97)-AVSN, SAE1 and UBA2 (1–550) were crystallized, so residues not observed in electron density were presumed disordered.
Cross-references: PDB:3KYD
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 218	to 234
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contained SUMO1(19–97)-AMSN, SAE1 amino acids (aa) 9–180 and 205–345, and UBA2 aa 5–217, 235–291, 305–548 and 608–640. As full-length proteins were used in crystallization, residues not observed in electron density were presumed disordered.
Cross-references: PDB:3KYC
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 549	to 607
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contained SUMO1(19–97)-AMSN, SAE1 amino acids (aa) 9–180 and 205–345, and UBA2 aa 5–217, 235–291, 305–548 and 608–640. As full-length proteins were used in crystallization, residues not observed in electron density were presumed disordered.
Cross-references: PDB:3KYC
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 198	to 217
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contained SUMO1(19–97)-AMSN, SAE1 amino acids (aa) 9–180 and 205–345, and UBA2 aa 5–217, 235–291, 305–548 and 608–640. As full-length proteins were used in crystallization, residues not observed in electron density were presumed disordered.
The final model includes SUMO1(20–97)-AVSN, SAE1 aa 25–183 and 204–345 and UBA2 aa 4–197, 240–290, 309–336 and 345–548. SUMO1(1–97)-AVSN, SAE1 and UBA2 (1–550) were crystallized, so residues not observed in electron density were presumed disordered.
The X-ray evidence shows there is a structure transition between the open and close conformation of the complex. The authors referred as closed conformation the structure formed by the E1~SUMO1-AVSN complex, whereas mention as open conformation the structure that forms the E1/SUMO1-AMSN complex.
Cross-references: PDB:3KYC
PDB:3KYD
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 198	to 217
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contained SUMO1(19–97)-AMSN, SAE1 amino acids (aa) 9–180 and 205–345, and UBA2 aa 5–217, 235–291, 305–548 and 608–640. As full-length proteins were used in crystallization, residues not observed in electron density were presumed disordered.
The final model includes SUMO1(20–97)-AVSN, SAE1 aa 25–183 and 204–345 and UBA2 aa 4–197, 240–290, 309–336 and 345–548. SUMO1(1–97)-AVSN, SAE1 and UBA2 (1–550) were crystallized, so residues not observed in electron density were presumed disordered.
The X-ray evidence shows there is a structure transition between the open and close conformation of the complex. The authors referred as closed conformation the structure formed by the E1~SUMO1-AVSN complex, whereas mention as open conformation the structure that forms the E1/SUMO1-AMSN complex.
Cross-references: PDB:3KYC
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 607	to 640
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Another notable difference was that E1 amino acids 607–640 of UBA2 were observed in contacts with SUMO1 via a C-terminal SIM motif (aa 632–640; ELDDVIALD; Supplemental Fig. 2) although the functional significance of the SIM remains unclear because amino acids 550–640 are dispensible for human E1 activity in vitro and for yeast E1 function in vivo in S. cerevisiae9.
Cross-references: PDB:3KYC
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 608	to 640
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows this region is ordered in the called open conformation of the E1/SUMO1-AMSN complex.
Cross-references: PDB:3KYC
Protein: DP00486 (UniProt Q9UBT2)
Region: residues 608	to 640
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows this region is ordered in the called open conformation of the E1/SUMO1-AMSN complex.
Cross-references: PDB:3KYC
Protein: DP00487 (UniProt P09938)
Region: residues 360	to 399
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered.
The Y2 model includes residues 26–359, and the Y4 model includes residues 11–90, 100–263, and 275–295.
Cross-references: PDB:1JK0
Protein: DP00488 (UniProt P49723)
Region: residues 296	to 345
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered.
No electron density is present for the C-terminal 41 residues of Y2 and 51 residues of Y4, suggesting that these regions are disordered.
Cross-references: PDB:1JK0
Protein: DP00488 (UniProt P49723)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:1JK0
Protein: DP00488 (UniProt P49723)
Region: residues 264	to 274
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows this region lacks electron density, indicating it is disordered.
No electron density was present for Y4 residues 91–99 and 264–274.
Cross-references: PDB:1JK0
Protein: DP00489 (UniProt P21793)
Region: residues 31	to 51
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No ordered density was observed for either the 14-aa propeptide (see Supporting Methods) or residues 1-21 of the mature protein, which contain the GAG attachment site.
Cross-references: PDB:1XCD
PDB:1XEC
PDB:1XKU
Protein: DP00489 (UniProt P21793)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
No ordered density was observed for either the 14-aa propeptide (see Supporting Methods) or residues 1-21 of the mature protein, which contain the GAG attachment site.
Protein: DP00490 (UniProt O88900)
Region: residues 361	to 435
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The plot of the PIR pattern, shown in Fig. 2, displays no trace of the bell shape associated with compact, globular particles.
All these observations and simple calculations support the view of PIR as an unfolded molecule with little or no residual structure in solution.
Protein: DP00490 (UniProt O88900)
Region: residues 361	to 435
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of Grb14 PIR exhibits characteristics typical of a random coil, like the large negative ellipticity at 200 nm and the low ellipticity at 185 nm.
Protein: DP00491 (UniProt Q62165)
Region: residues 652	to 748
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The secondary structure content of the N-terminal extracellular domain of beta-dystroglycan (a recombinant fragment extending from positions 654 to 750) has been quantitatively determined by means of CD and FTIR spectroscopies. The elements of secondary structure, namely an 8-10 residue long alpha-helix (10%) and two beta-strands (24%) have been assigned to specific amino acid sequences by means of a GOR constrained prediction method. The remaining 66% of the whole sequence is classified as turns or unordered.
Protein: DP00491 (UniProt Q62165)
Region: residues 652	to 748
Annotation: molten globule (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
The secondary structure content of the N-terminal extracellular domain of beta-dystroglycan (a recombinant fragment extending from positions 654 to 750) has been quantitatively determined by means of CD and FTIR spectroscopies. The elements of secondary structure, namely an 8-10 residue long alpha-helix (10%) and two beta-strands (24%) have been assigned to specific amino acid sequences by means of a GOR constrained prediction method. The remaining 66% of the whole sequence is classified as turns or unordered.
Protein: DP00491 (UniProt Q62165)
Region: residues 652	to 748
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
All these data provide compelling evidence that  β-DG(654−750) molecules represent an ensemble of different populations of disordered polypeptide chains.
Cross-references: BMRB:5743
Protein: DP00491 (UniProt Q62165)
Region: residues 689	to 717
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The binding of β-DG(654−750) to the C-terminal region of the α subunit, α-DG(485−620), has been investigated, showing that the region of β-DG(654−750) between residues 691 and 719 is involved in the interaction.
Protein: DP00492 (UniProt P10275)
Region: residues 142	to 485
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In aqueous solution, the AR polypeptide showed relatively little stable secondary structure. The dominant feature of the CD spectrum was a minimum at around 200 nm, which is characteristic of a non-ordered polypeptide (Fig. 2A).
Protein: DP00492 (UniProt P10275)
Region: residues 142	to 485
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In aqueous solution, the AR polypeptide
showed relatively little stable secondary structure. The dominant feature of the CD spectrum was a minimum at around 200
nm, which is characteristic of a non-ordered polypeptide (Fig.
2A). In contrast, in the presence of increasing amounts of the
hydrophobic solvent TFE, the CD spectrum was characterized
by minima at 208 and 222 nm, indicative of a significant
proportion of alfa-helical structure (Fig. 2A). 
The analysis indicates that the helical content increased from 13 to 40% with a reduction in the turn and other
structure contents from 32 to 20% and from 36 to 25%, respectively, as the TFE concentration was increased from 0 to 50%
(Fig. 2B).
Protein: DP00492 (UniProt P10275)
Region: residues 142	to 485
Annotation: disorder (Structural state)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
The fluorescence spectrum for AR4 is characterized by an emission maximum at 343 nm, due to the tryptophan residues, and a shoulder at 309 nm, resulting from tyrosine emission (Fig. 3A). Fig. 3B shows that in the presence of increasing amounts of acrylamide the fluorescence intensity for the tryptophan maximum after excitation at 295 nm was reduced. From the linear plot, a Stern-Volmer constant (Ksv) of 10.8 M1 was calculated, indicating that both tryptophans have a high degree of exposure to solvent and behave in an identical fashion (35).
Protein: DP00492 (UniProt P10275)
Region: residues 142	to 485
Annotation: disorder to order (Structural transition)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
In the presence of up to 3 M TMAO
there was an increase in the quantum yield, the tryptophan
emission maximum blue shifted to 336 nm, and the shoulder
due to tyrosine fluorescence was lost (Fig. 3A). A similar trend
was observed with 10 and 20% TFE (data not shown). These
results indicate that the two tryptophan residues become less
solvent-exposed, and there is an increase in the energy transfer
from tyrosine to tryptophan residues, consistent with the AR
polypeptide becoming more structured.
Taken together the
spectroscopy analysis indicates that the AR transactivation
domain is structurally flexible and capable of a adopting a more
folded conformation in the presence of the alcohol TFE or the
natural osmolyte TMAO.
Protein: DP00492 (UniProt P10275)
Region: residues 142	to 485
Annotation: molecular adaptor activity (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In the presence of RAP74-CTD
(amino acids 363–517), the AR polypeptide was markedly less
susceptible to cleavage by trypsin (Fig. 7A) and chymotrypsin
(Fig. 8A).
We interpret these
results as providing evidence for at least in part a conformational change in the AR4 polypeptide upon binding of RAP74-
CTD, which leads to a protease resistant state.
Protein: DP00492 (UniProt P10275)
Region: residues 142	to 485
Annotation: disorder to order (Structural transition)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
In the presence of RAP74-CTD
(amino acids 363–517), the AR polypeptide was markedly less
susceptible to cleavage by trypsin (Fig. 7A) and chymotrypsin
(Fig. 8A).
In the presence of increasing concentrations of TMAO or TFE, AR4 became less susceptible to
trypsin cleavage (Fig. 7, B and C).
We interpret these
results as providing evidence for at least in part a conformational change in the AR4 polypeptide upon binding of RAP74-
CTD, which leads to a protease resistant state.
Protein: DP00492 (UniProt P10275)
Region: residues 142	to 485
Annotation: protein binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The GST-AR4 fusion protein was extremely sensitive to proteolytic cleavage, and treatment with trypsin, chymotrypsin, or endoproteinase Glu-C resulted in the generation of a series of stable fragments of relative molecular mass 24,000–30,000 Da, representing the
GST moiety (Figs. 7 and 8). In the presence of RAP74-CTD (amino acids 363–517), the AR polypeptide was markedly less susceptible to cleavage by trypsin (Fig. 7A) and chymotrypsin (Fig. 8A).
Protein: DP00492 (UniProt P10275)
Region: residues 142	to 485
Annotation: disorder (Structural state)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
Using Fourier transform infrared (FTIR), we tested whether this interaction can induce structure in the AR AF1. 
When the sum of the second-derivative spectra of AF1 and RAP74-CTD are compared with the spectrum of the AF1/RAP74-CTD mixture (Figure 2B), it is evident that the helical content is higher in the AF1/RAP74-CTD mixture than in the summation of the AF1 and RAP74-CTD spectra, suggesting that these changes are not just additive. Comparison of the second-derivative spectra of AF1 with and without RAP74-CTD present indicated a significant increase in helical content in AF1 when mixed with RAP74-CTD (Figure 3A), suggesting that interaction with RAP74-CTD leads to imposition of helical structure on the AF1 domain.
Our results indicate that the AF1 domain has little helical structure until it encounters RAP74. This interaction leads to formation of more helical conformation in AR AF1.  This appears to come as a result of the loss of β-sheet along with an accumulation of small losses of turns, bends, and coil.
Our findings herein, showing that AR AF1 adopts a more helical conformation when bound to RAP74, clearly indicate that AF1 can acquire helical structure through an induced-fit mechanism, when it encounters a specific binding partner.
Protein: DP00492 (UniProt P10275)
Region: residues 142	to 485
Annotation: disorder to order (Structural transition)
Evidence: Fourier-transform infrared spectroscopy evidence used in manual assertion
Supporting statements:
Using Fourier transform infrared (FTIR), we tested whether this interaction can induce structure in the AR AF1. 
When the sum of the second-derivative spectra of AF1 and RAP74-CTD are compared with the spectrum of the AF1/RAP74-CTD mixture (Figure 2B), it is evident that the helical content is higher in the AF1/RAP74-CTD mixture than in the summation of the AF1 and RAP74-CTD spectra, suggesting that these changes are not just additive. Comparison of the second-derivative spectra of AF1 with and without RAP74-CTD present indicated a significant increase in helical content in AF1 when mixed with RAP74-CTD (Figure 3A), suggesting that interaction with RAP74-CTD leads to imposition of helical structure on the AF1 domain.
Our results indicate that the AF1 domain has little helical structure until it encounters RAP74. This interaction leads to formation of more helical conformation in AR AF1.  This appears to come as a result of the loss of β-sheet along with an accumulation of small losses of turns, bends, and coil.
Our findings herein, showing that AR AF1 adopts a more helical conformation when bound to RAP74, clearly indicate that AF1 can acquire helical structure through an induced-fit mechanism, when it encounters a specific binding partner.