LiteFold/DisProt huggingface dataset:
Protein: DP02262 (UniProt P42226)
Region: residues 783	to 814
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Altogether, the NMR structure indicates that the coactivator recognition mechanism by STAT6 occurs by the formation of a complex in which two folded regions are connected by a linker that adopts an extended conformation
The NMR structure of the NCoA1257–385/STAT6783–814 complex (PDB ID: 5NWM), is of high quality (Table SI 4).
Cross-references: PDB:5NWM
Protein: DP02262 (UniProt P42226)
Region: residues 790	to 799
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
the NMR structure indicates that the coactivator recognition mechanism by STAT6 occurs by the formation of a complex in which two folded regions are connected by a linker that adopts an extended conformation.
Cross-references: PDB:5NWM
Protein: DP02262 (UniProt P42226)
Region: residues 783	to 793
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In this crystal structure the residues located in the N-terminal part (Gly783 - Pro793) are not ordered indicating that this region is too dynamic to be resolved in the crystal (SI Fig. 3).
Cross-references: PDB:5NWX
Protein: DP02262 (UniProt P42226)
Region: residues 786	to 808
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A subset of STAT6783–814 backbone amide resonances becomes well dispersed in the presence of the binding partner (Fig. 3A). These changes are indicative of a well-structured region within the bound STAT6783–814 peptide.
Regarding the STAT6783–814 peptide in the bound form, the analysis from chemical shifts, 3JHNHα couplings and the relative weight of interresidual NOEs (Fig. 2C) suggests that the STAT6783–814 peptide presents a flexible N-terminal tail, followed by an α-helix in the region Ile786-Ile790 whose population increases from around 10% in the free form to close to 100% upon binding to NcoA1 PAS-B (Fig. 2C) (SI Fig. 9). Then a short extended linker follows and finally the second α-helix (Glu799-Glu808) (Fig. 2A,B) whose population increases from 30% to close to 100%.
Given that existing prestructured motifs are enhanced in the bound form, the data suggest that the recognition of the coactivator by STAT6 occurs by a conformational selection25 mechanism regarding the secondary structure.
Cross-references: PDB:5NWM
Protein: DP02262 (UniProt P42226)
Region: residues 786	to 790
Annotation: transcription coactivator binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Regarding the STAT6783–814 peptide in the bound form, the analysis from chemical shifts, 3JHNHα couplings and the relative weight of interresidual NOEs (Fig. 2C) suggests that the STAT6783–814 peptide presents a flexible N-terminal tail, followed by an α-helix in the region Ile786-Ile790 whose population increases from around 10% in the free form to close to 100% upon binding to NcoA1 PAS-B (Fig. 2C) (SI Fig. 9). Then a short extended linker follows and finally the second α-helix (Glu799-Glu808) (Fig. 2A,B) whose population increases from 30% to close to 100%.
Given that existing prestructured motifs are enhanced in the bound form, the data suggest that the recognition of the coactivator by STAT6 occurs by a conformational selection25 mechanism regarding the secondary structure.
Cross-references: PDB:5NWM
Protein: DP02262 (UniProt P42226)
Region: residues 799	to 808
Annotation: transcription coactivator binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Regarding the STAT6783–814 peptide in the bound form, the analysis from chemical shifts, 3JHNHα couplings and the relative weight of interresidual NOEs (Fig. 2C) suggests that the STAT6783–814 peptide presents a flexible N-terminal tail, followed by an α-helix in the region Ile786-Ile790 whose population increases from around 10% in the free form to close to 100% upon binding to NcoA1 PAS-B (Fig. 2C) (SI Fig. 9). Then a short extended linker follows and finally the second α-helix (Glu799-Glu808) (Fig. 2A,B) whose population increases from 30% to close to 100%.
Given that existing prestructured motifs are enhanced in the bound form, the data suggest that the recognition of the coactivator by STAT6 occurs by a conformational selection25 mechanism regarding the secondary structure.
Cross-references: PDB:5NWM
Protein: DP02262 (UniProt P42226)
Region: residues 791	to 798
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Regarding the STAT6783–814 peptide in the bound form, the analysis from chemical shifts, 3JHNHα couplings and the relative weight of interresidual NOEs (Fig. 2C) suggests that the STAT6783–814 peptide presents a flexible N-terminal tail, followed by an α-helix in the region Ile786-Ile790 whose population increases from around 10% in the free form to close to 100% upon binding to NcoA1 PAS-B (Fig. 2C) (SI Fig. 9). Then a short extended linker follows and finally the second α-helix (Glu799-Glu808) (Fig. 2A,B) whose population increases from 30% to close to 100%.
Given that existing prestructured motifs are enhanced in the bound form, the data suggest that the recognition of the coactivator by STAT6 occurs by a conformational selection25 mechanism regarding the secondary structure.
Cross-references: PDB:5NWM
Protein: DP02263 (UniProt P32120)
Region: residues 352	to 390
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structure of beta-arrestin2 in complex with D6Rpp shows this region lacks electron density, indicating it is disordered. 
Cross-references: PDB:8J8V
EMDB:36081
Protein: DP02263 (UniProt P32120)
Region: residues 409	to 420
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structure of beta-arrestin2 in complex with D6Rpp shows this region lacks electron density, indicating it is disordered. 
Cross-references: PDB:8J8V
EMDB:36081
Protein: DP02263 (UniProt P32120)
Region: residues 351	to 420
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The cryo-EM structure of beta-arrestin2 in complex with M2Rpp shows this region lacks electron density, indicating it is disordered. 
Cross-references: PDB:8J8R
EMDB:36078
Protein: DP02264 (UniProt Q12306)
Region: residues 1	to 23
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Similar to Sumo-1, the data indicated that the first 23 residues at the N-terminus were disordered.
Cross-references: pdb:1l2n
Protein: DP02267 (UniProt Q8IVG9)
Region: residues 1	to 24
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Unstructured in aqueous solution but adopts a helical conformation at the presence of 30% TFE. NMR data are only available for the structure in 30% TFE solution (PDB:1Y32).
Protein: DP02267 (UniProt Q8IVG9)
Region: residues 1	to 24
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In the absence of TFE, the CD spectrum shows strong negative dichroism below 200 nm, indicative of a small degree of ordering in the peptide. On addition of TFE, changes diagnostic of conformational equilibrium between unordered structures and helical conformations of humanin in solution take place in the CD spectra.
Protein: DP02269 (UniProt Q9Y6K9)
Region: residues 252	to 272
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The secondary structure of IKKγ is shown above the residues, where dark blue arrows indicate α helices and dashed dark blue lines indicate disordered regions
Cross-references: PDB:3CL3
Protein: DP02269 (UniProt Q9Y6K9)
Region: residues 150	to 192
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The secondary structure of IKKγ is shown above the residues, where dark blue arrows indicate α helices and dashed dark blue lines indicate disordered regions.
Cross-references: PDB:3CL3
Protein: DP02269 (UniProt Q9Y6K9)
Region: residues 1	to 43
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Proteins starting at residue 1 produced NMR spectra with ∼40 very intense crosspeaks with poor dispersion (data not shown), whereas proteins starting at residue 44 did not display this characteristic. This finding was attributed to a disordered N terminus of ∼40 residues; therefore, residue 44 was selected as the N-terminal start site for crystallization constructs.
Protein: DP02271 (UniProt P29131)
Region: residues 68	to 79
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Full domain structure depicted in Figure 6.
Cross-references: BMRB:5984
PDB:1UTA
Protein: DP02271 (UniProt P29131)
Region: residues 124	to 215
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Full domain structure depicted in Figure 6.
Cross-references: BMRB:5984
PDB:1UTA
Protein: DP02271 (UniProt P29131)
Region: residues 94	to 116
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Full domain structure depicted in Figure 6.
Cross-references: BMRB:5984
PDB:1UTA
Protein: DP02272 (UniProt Q7KLE5)
Region: residues 1	to 26
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminus is disordered before residue 26, and the C-terminus is disordered beyond residue 242.
Cross-references: PDB:1URU
Protein: DP02272 (UniProt Q7KLE5)
Region: residues 1	to 26
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
On lipid binding, the helical content of the N-BAR domain of amphiphysin increased, as shown by circular dichroism spectroscopy (fig. S2B), which suggested that the N-terminus folded into an extra helix. This increase in helical content is not seen when residues 1 to 26 are deleted.
Protein: DP02272 (UniProt Q7KLE5)
Region: residues 158	to 170
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The positively charged loop between helices 2 and 3 found at the extreme ends of the dimer is flexible and poorly ordered (residues 158 to 165 in dAmph) and is the location of a splice variant in mammalian amphiphysin2 (residues 173 to 205 in Fig. 1E).
The deposited data shows the flexible region spans from 158 to the 170 residue.
Cross-references: PDB:1URU
Protein: DP02272 (UniProt Q7KLE5)
Region: residues 158	to 170
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The positively charged loop between helices 2 and 3 found at the extreme ends of the dimer is flexible and poorly ordered (residues 158 to 165 in dAmph) and is the location of a splice variant in mammalian amphiphysin2 (residues 173 to 205 in Fig. 1E).
The deposited data shows the flexible loop spans from 158 to the 170 residue.
Cross-references: PDB:1URU
Protein: DP02272 (UniProt Q7KLE5)
Region: residues 160	to 164
Annotation: lipid tube assembly (Biological process)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
To test if this tubulating ability is due to the Drosophila amphiphysin BAR domain, we mutated pairs of basic residues to glutamates, Lys161 + Lys163 on the disordered loop between helices 2 and 3 (mut1) and Lys137 + Arg140 on the concave face (mut2). Neither of these mutations interfered with the structure, and both double-mutants reduced the binding to liposomes; the quadruple-mutant (mut3) was more effective (Fig. 2A). These mutants also effectively inhibited the tubulation of liposomes as assessed by electron microscopy (Fig. 2B). At higher concentrations, the double-mutants showed some tubulation, whereas the quadruple-mutant did not.
Protein: DP02272 (UniProt Q7KLE5)
Region: residues 1	to 26
Annotation: lipid binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
Deletion of residues 1 to 26 of Drosophila amphiphysin or residues 1 to 27 in mammalian amphiphysin1, or mutation of Phe9 to glutamate, reduced liposome binding as expected (16), but these proteins still tubulated at high concentrations (Fig. 2, B and E).
Lipid binding was assessed by electron microscopy and sedimentation assay with total bovine brain lipids.
Protein: DP02290 (UniProt Q92905)
Region: residues 198	to 218
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
It is noteworthy that the lack of electron density for the CSN5 portion consisting of residues 197–219 [corresponding to Ins-2 in the structure of associated molecule with the SH3 domain of STAM (signal transducing adapter molecule) deubiquitinase (AMSH-LP) (20)] prevented accurate modeling and analysis of this segment.
Correct positioning of the K63-Ub2 isopeptide bond in the long recognition groove of AMSH-LP is ensured by interactions between AMSH-LP [in particular, the Ins-1 region, the Ins-2 loop (disordered in CSN5), and the segment between these two insertions) and the proximal and distal ubiquitins (SI Appendix, Fig. S2)].
Cross-references: PDB:4F7O
Protein: DP02290 (UniProt Q92905)
Region: residues 284	to 295
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered residues are represented by dashed lines.
Cross-references: PDB:4D10
PDB:4D18
Protein: DP02291 (UniProt P04486)
Region: residues 412	to 490
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
VP16 was shown before to be unstructured in solution (16, 32, 33). We confirm this notion by the absence of NOE contacts that are indicative for secondary structure elements.
The (1H,15N)-HSQC spectrum of VP16ad shows a small dispersion of intense signals in the proton dimension (<1 ppm), indicative for a lack of secondary structure.
HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: BMRB:6099
Protein: DP02291 (UniProt P04486)
Region: residues 456	to 490
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR structural studies demonstrate that VP16C is disordered in the free state, and forms a 9-residue α-helix involving residues Asp472 to Thr480 in complex with Tfb1.
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Protein: DP02291 (UniProt P04486)
Region: residues 456	to 490
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Addition of VP16C (VP16456−490) to 15N-labeled Tfb11−115 produced changes in 1H and 15N chemical shifts for several signals of Tfb11−115 in the 2D 1H−15N HSQC spectra (Figure 1).
The structure of the Tfb11−115/VP16C complex is well defined by the NMR data (Figure 2).
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Protein: DP02291 (UniProt P04486)
Region: residues 456	to 490
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The binding interface of the Tfb1/VP16C complex comprises strands β5, β6 and β7 and the loop connecting β5 and β6 of Tfb1 and the 9-residue α-helix of VP16C (Asp472−Thr480).
Addition of VP16C (VP16456−490) to 15N-labeled Tfb11−115 produced changes in 1H and 15N chemical shifts for several signals of Tfb11−115 in the 2D 1H−15N HSQC spectra (Figure 1).
The structure of the Tfb11−115/VP16C complex is well defined by the NMR data (Figure 2).
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: PDB:2K2U
Protein: DP02291 (UniProt P04486)
Region: residues 412	to 456
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
By this method, VP16C bound to Tfb1 with an apparent Kd of 360 ± 40 nM and VP16N bound to Tfb1 with an apparent Kd of 1000 ± 100 nM (Table 1). These results suggested that both subdomains of the VP16TAD were capable of interacting with Tfb1, and the Kd obtained for the Tfb1/VP16C complex is very similar to the Kd observed between Tfb1 and the p53TAD2 (390 nM).
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Protein: DP02291 (UniProt P04486)
Region: residues 456	to 490
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
By this method, VP16C bound to Tfb1 with an apparent Kd of 360 ± 40 nM and VP16N bound to Tfb1 with an apparent Kd of 1000 ± 100 nM (Table 1). These results suggested that both subdomains of the VP16TAD were capable of interacting with Tfb1, and the Kd obtained for the Tfb1/VP16C complex is very similar to the Kd observed between Tfb1 and the p53TAD2 (390 nM).
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Protein: DP02291 (UniProt P04486)
Region: residues 456	to 490
Annotation: molecular function activator activity (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
By this method, VP16C bound to Tfb1 with an apparent Kd of 360 ± 40 nM and VP16N bound to Tfb1 with an apparent Kd of 1000 ± 100 nM (Table 1). These results suggested that both subdomains of the VP16TAD were capable of interacting with Tfb1, and the Kd obtained for the Tfb1/VP16C complex is very similar to the Kd observed between Tfb1 and the p53TAD2 (390 nM).
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Protein: DP02291 (UniProt P04486)
Region: residues 412	to 490
Annotation: molecular function activator activity (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
By this method, VP16C bound to Tfb1 with an apparent Kd of 360 ± 40 nM and VP16N bound to Tfb1 with an apparent Kd of 1000 ± 100 nM (Table 1). These results suggested that both subdomains of the VP16TAD were capable of interacting with Tfb1, and the Kd obtained for the Tfb1/VP16C complex is very similar to the Kd observed between Tfb1 and the p53TAD2 (390 nM).
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Protein: DP02291 (UniProt P04486)
Region: residues 412	to 490
Annotation: disorder to order (Structural transition)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492.
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r005
Protein: DP02291 (UniProt P04486)
Region: residues 454	to 490
Annotation: protein binding (Molecular function)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492.
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r028
Protein: DP02291 (UniProt P04486)
Region: residues 412	to 490
Annotation: protein binding (Molecular function)
Evidence: curator inference used in manual assertion
Supporting statements:
IDR is 100% identical to the Human herpesvirus 1 (strain 17), UniProtKB:P06492.
The VP16 gene fragment used in this publication was derived from the Human herpesvirus 1 KOS strain. HSV-1 VP16 amino acid sequences of the KOS and F strains are identical for all 490 residues and differ from strain 17 by only two amino acid substitutions (Asp-Asn at position 13 and Ala-Thr at position 124).
Cross-references: DisProt:DP01642r027
DisProt:DP01642r026
DisProt:DP01642r006
PDB:2PHE
PDB:2PHG