LiteFold/DisProt huggingface dataset:
Protein: DP01308 (UniProt O60828)
Region: residues 238	to 260
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The binary complex of PQBP1-CT43 and U5–15kD was obtained by mixing the proteins at a 1:5 molar ratio (U5–15kD to PQBP1-CT43). The crystals belong to space group P2 and contain four heterodimeric complexes in the asymmetric unit. The crystal structure of the binary complex was refined to a resolution of 2.1 Å with an Rwork/Rfree value of 19/25% (Table 1). The refined model of the PQBP1-CT43 in the complex consists of the residues 238–260: it lacks the 15 N-terminal residues (residues 223–237; KRNEAKTGADTTAAG) and the 5 C-terminal residues (residues 261–265; TKQQD) owing to conformational flexibility (Fig. 2a).
Cross-references: PDB:4BWS
PDB:4BWQ
PDB:4CDO
Protein: DP01308 (UniProt O60828)
Region: residues 1	to 265
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In the present study, we demonstrate that PQBP-1 is composed of a large unstructured region and a small folded core. Intriguingly, the large unstructured region encompasses two functional domains: a polar amino acid rich domain and a C-terminal domain. These findings suggest that PQBP-1 belongs to the family of intrinsically unstructured/disordered proteins.
We demonstrate that PQBP-1 is composed of a large unstructured region and a small folded core. The large unstructured region encompasses two functional domains, the PRD and the CTD.
To determine the secondary structure of the full-length PQBP-1, we recorded the far-UV CD spectrum (Fig. 3A). The CD spectrum displays a minimum at 204 nm with negative ellipticity of − 4700 deg cm2 dmol− 1, which is characteristic of a protein in largely unfolded conformations, whereas the spectral features indicative of α-helices or β-sheets are absent (Fig. 3A).
Protein: DP01308 (UniProt O60828)
Region: residues 1	to 265
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the present study, we demonstrate that PQBP-1 is composed of a large unstructured region and a small folded core. Intriguingly, the large unstructured region encompasses two functional domains: a polar amino acid rich domain and a C-terminal domain. These findings suggest that PQBP-1 belongs to the family of intrinsically unstructured/disordered proteins.
We demonstrate that PQBP-1 is composed of a large unstructured region and a small folded core. The large unstructured region encompasses two functional domains, the PRD and the CTD.
The 1H–15N HSQC spectrum also revealed the largely unfolded conformation of full-length PQBP-1, as judged by the numerous sharp resonances of backbone amides which overlap within a narrow 1H chemical shift range from 7.8 to 8.8 ppm (Fig. 4A). In addition to the sharp resonances, however, the HSQC spectrum for the full-length PQBP-1 showed several well-dispersed peaks typical of a folded conformation. The HSQC thus indicates that the full-length PQBP-1 contains a small structured region as well as a large unstructured region.
Protein: DP01308 (UniProt O60828)
Region: residues 94	to 265
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H–15N HSQC spectra of PQBP-1-PR and PQBP-1-CT showed the sharp resonances of backbone amides clustered within 7.8–8.8 ppm (1H dimension), indicating highly flexible, unfolded conformations (Fig. 4C and D). In contrast, the backbone amide resonances of PQBP-1-WW are dispersed from 7.0 to 9.8 ppm, which is characteristic of folded proteins (Fig. 4B).
Therefore, the comparison of the HSQC spectra of full-length PQBP-1 and its fragments revealed that the PRD and CTD are largely unstructured in PQBP-1, and the WWD is involved in the structured region of PQBP-1.
Region corresponding to fragments PQBP-1-PR (94–176) and PQBP-1-CT (193–265).
Protein: DP01308 (UniProt O60828)
Region: residues 94	to 265
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-UV CD spectrum of PQBP-1-PR and -CT lacked the typical signature of secondary structure, exhibiting instead only a negative signal at 200 nm (Fig. 3C and D). 
These CD data support the conclusion derived from NMR that PQBP-1 comprises the folded region in the WWD and the large unstructured regions in the PRD and CTD.
Region corresponding to fragments PQBP-1-PR (94–176) and PQBP-1-CT (193–265).
Protein: DP01308 (UniProt O60828)
Region: residues 1	to 265
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
Binding of U5-15kD is one of the functions of PQBP-1. To determine the affinity of PQBP-1 to U5-15kD, we decided to analyze this interaction by surface plasmon resonance (Fig. 6A). We determined the apparent association rate constant and dissociation rate constant for the complex between PQBP-1 and U5-15kD. PQBP-1 exhibited a fast association rate with U5-15kD (ka = 4.1 × 103 M− 1 s− 1) and a slow dissociation rate (kd = 2.5 × 10− 3 s− 1). Hence, the dissociation constant (KD = kd / ka) was calculated to be 0.6 μM.
Protein: DP01308 (UniProt O60828)
Region: residues 193	to 265
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
The binding was confirmed by GST pull-down assay and gel-filtration chromatography. The GST pull-down assay shows that either GST-PQBP-1 or GST-PQBP-1-CT binds to U5-15kD (Fig. 6B).
Protein: DP01308 (UniProt O60828)
Region: residues 1	to 265
Annotation: protein binding (Molecular function)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
The binding was confirmed by GST pull-down assay and gel-filtration chromatography. The GST pull-down assay shows that either GST-PQBP-1 or GST-PQBP-1-CT binds to U5-15kD (Fig. 6B).
Protein: DP01309 (UniProt P50750)
Region: residues 87	to 98
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The loops between residues 50-55, 87-98 and 259-267 are missing in the 2.5A structure as well as a part of the activation segment residues 176-182.  
The major differences occur in loop regions and include the loop before the αC helix, corresponding to a CycA contact region in the CDK2/CycA complex, the
loop between β4 and β5 where CDK9 has an insertion compared with CDK2 (not defined by electron density (residues 87–98)), the loop between the  αD and  αE helices (residues 114–121), part of the activation segment (where additional residues 179–182 are not defined) and the loop between  αG and  αH residues 259–267.
Cross-references: PDB:3BLR
PDB:3BLH
PDB:3BLQ
Protein: DP01309 (UniProt P50750)
Region: residues 328	to 372
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In these structures, electron density for the C-terminal sequence of CDK9 is either missing after residue 325 (Baumli et al., 2008) or extends away from the CDK9 fold and adopts a structure that is determined by crystal contacts (Tahirov et al., 2010; Figure S4).
The electron density gradually weakens after residue 327, and further residues could not be built with confidence. This result indicates that the CDK9 C-terminal tail is inherently flexible.
(I) Apo CDK9 has a flexible C-terminal tail.
(V) ADP is released and the kinase returns to its apo state with a flexible C-terminal tail.
Cross-references: PDB:4EC9
Protein: DP01309 (UniProt P50750)
Region: residues 328	to 338
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The CDK9 C-Terminal Tail Becomes Structured upon Binding to an Active Kinase Conformation.
The resulting crystal structure, solved at 3.6 Å resolution, shows unambiguous electron density for the inhibitor and 11 additional CDK9 C-terminal residues as compared with the structure of CDK9FL/cyclin T259 (Table 2; Figures 3B–3D).
CDK9 adopts a closed state upon DRB binding in which the N-terminal lobe is rotated by 8° with respect to the apo or ATP-bound structure.
This closed state is stabilized in the context of CDK9FL by folding of the C-terminal tail over the ATP binding site (Figures 3B and 3D).
Cross-references: PDB:4EC8
PDB:4EC9
Protein: DP01309 (UniProt P50750)
Region: residues 345	to 357
Annotation: nucleus localization (Biological process)
Evidence: fluorescence quantification assay evidence used in manual assertion
Supporting statements:
 In addition to the catalityc activity, nuclear localization of Cdk9 protein requires the presence of the phospho-acceptor sites at the C-terminus tail.
To test this hypothesis, we constructed two C-terminal mutants Cdk9Δ337 and Cdk9ΔST both lacking the Ser/Thr residues previously shown to represent the major phospho-acceptor sites of auto-phosphorylation. As shown in Figure 1, unlike the Cdk9wt GFP-fusion protein, both GFP-Cdk9Δ337 and GFP-Cdk9ΔST fusions failed to accumulate to the nucleus and the majority of transfected cells showed a fluorescence signal in both nuclear and cytoplasmic compartments. These results provide evidences that Cdk9 nuclear localization is dependent upon the catalytic activity of the kinase and the presence of the major phospho-acceptor residues required for auto-phosphorylation.
Protein: DP01309 (UniProt P50750)
Region: residues 259	to 273
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB evidence shows this region lacks electron density, indicating it is disordered
Cross-references: PDB:3TNH
Protein: DP01309 (UniProt P50750)
Region: residues 88	to 97
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PDB evidence shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:3TNI 
PDB:3TNH
Protein: DP01309 (UniProt P50750)
Region: residues 330	to 372
Annotation: kinase activity (Molecular function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
At an ATP concentration of 100 μM, CDK9330 has only 30% of the kinase activity of the full-length protein (Figure S1A available online). Further enzymatic analysis revealed that this difference in activity does not result from differences in affinity toward GST-CTD, because both CDK9330 and CDK9FL have very similar KM,app (apparent KM value at a fixed concentration of the second substrate) values for this substrate (21.3 ± 3.7 μM versus 24.3 ± 2.7 μM, respectively; Figure S1B).
Furthermore, the dependence of KM as well as Vmax with respect to the ATP substrate indicates that the C-terminal tail influences ATP binding and catalysis (Cornish-Bowden, 2004).
Protein: DP01310 (UniProt Q8WUP2)
Region: residues 5	to 19
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Migfilin Residues 5-19 Mediate Binding to FLNa
Protein: DP01310 (UniProt Q8WUP2)
Region: residues 1	to 85
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N-HSQC spectrum of migfilin-(1-85) (supplemental Fig. S1) has chemical shifts typical of an unstructured species (30). Moreover, heteronuclear 1H-(15N)-NOE experiments showed complete peak inversion for nearly all the N-H cross-peaks, which implies that the protein chain is extremely flexible (31).
Protein: DP01311 (UniProt Q6NUK1)
Region: residues 50	to 78
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Regions that have low heteronuclear NOE values include H3 and adjacent loops (residues 50–78), the Ca2+-binding loop of EF-hand III (residues 99–109), as well as the C-terminal H9 (residues 159–170) (Fig. 3B and 3G).
Protein: DP01311 (UniProt Q6NUK1)
Region: residues 50	to 78
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We attempted to crystallize the apo NTD but were not successful. We then found, during measurements of NMR relaxation rates, that the apo NTD has very substantial internal dynamics, which explains the unsuccessful crystallization trials. The 1H-15N TROSY-HSQC spectra of the apo and Ca2+-bound NTD are completely different (Fig. S4A), indicating that the structural and/or dynamic properties of the two states are very different and that Ca2+ binding clearly triggers a major conformational switch in the protein.
The relaxation data for the Ca2+-bound NTD is very uniform (except for N- and C-terminus) (Fig. 3A, 3C and 3E), which is indicative of a rigid and compact structure where the structured segments of the protein tumble together in solution.
Regions that have low heteronuclear NOE values include H3 and adjacent loops (residues 50–78), the Ca2+-binding loop of EF-hand III (residues 99–109), as well as the C-terminal H9 (residues 159–170) (Fig. 3B and 3G).
Protein: DP01311 (UniProt Q6NUK1)
Region: residues 99	to 109
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Regions that have low heteronuclear NOE values include H3 and adjacent loops (residues 50–78), the Ca2+-binding loop of EF-hand III (residues 99–109), as well as the C-terminal H9 (residues 159–170) (Fig. 3B and 3G).
Protein: DP01311 (UniProt Q6NUK1)
Region: residues 99	to 109
Annotation: calcium ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The crystal structure of the Ca2-bound NTD shows a rigid and elongated architecture that contains three main structured regions: the N-terminal lobe (residues 22–87) and the C-terminal lobe (residues 88–152), each consisting of two Ca2+-bound EF hands, and a C-terminal helix (residues 159–170) (Fig. 1A).
Regions that have low heteronuclear NOE values include H3 and adjacent loops (residues 50–78), the Ca2+-binding loop of EF-hand III (residues 99–109), as well as the C-terminal H9 (residues 159–170) (Fig. 3B and 3G).
Cross-references: PDB:4N5X
Protein: DP01311 (UniProt Q6NUK1)
Region: residues 159	to 170
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Regions that have low heteronuclear NOE values include H3 and adjacent loops (residues 50–78), the Ca2+-binding loop of EF-hand III (residues 99–109), as well as the C-terminal H9 (residues 159–170) (Fig. 3B and 3G).
Protein: DP01311 (UniProt Q6NUK1)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of the Ca2+-bound NTD in the P3121 crystal was subsequently refined to 2.1 Å with good statistics (R = 17.67%, Rfree = 22.53%; full statistics in Table 1).
In the electron density map, however, only residues 22–176 were visible.
Cross-references: PDB:4N5X
Protein: DP01311 (UniProt Q6NUK1)
Region: residues 177	to 193
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of the Ca2+-bound NTD in the P3121 crystal was subsequently refined to 2.1 Å with good statistics (R = 17.67%, Rfree = 22.53%; full statistics in Table 1).
In the electron density map, however, only residues 22–176 were visible.
Cross-references: PDB:4N5X
Protein: DP01311 (UniProt Q6NUK1)
Region: residues 99	to 109
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We attempted to crystallize the apo NTD but were not successful. We then found, during measurements of NMR relaxation rates, that the apo NTD has very substantial internal dynamics, which explains the unsuccessful crystallization trials. The 1H-15N TROSY-HSQC spectra of the apo and Ca2+-bound NTD are completely different (Fig. S4A), indicating that the structural and/or dynamic properties of the two states are very different and that Ca2+ binding clearly triggers a major conformational switch in the protein.
The relaxation data for the Ca2+-bound NTD is very uniform (except for N- and C-terminus) (Fig. 3A, 3C and 3E), which is indicative of a rigid and compact structure where the structured segments of the protein tumble together in solution.
Regions that have low heteronuclear NOE values include H3 and adjacent loops (residues 50–78), the Ca2+-binding loop of EF-hand III (residues 99–109), as well as the C-terminal H9 (residues 159–170) (Fig. 3B and 3G).
Protein: DP01311 (UniProt Q6NUK1)
Region: residues 159	to 170
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We attempted to crystallize the apo NTD but were not successful. We then found, during measurements of NMR relaxation rates, that the apo NTD has very substantial internal dynamics, which explains the unsuccessful crystallization trials. The 1H-15N TROSY-HSQC spectra of the apo and Ca2+-bound NTD are completely different (Fig. S4A), indicating that the structural and/or dynamic properties of the two states are very different and that Ca2+ binding clearly triggers a major conformational switch in the protein.
The relaxation data for the Ca2+-bound NTD is very uniform (except for N- and C-terminus) (Fig. 3A, 3C and 3E), which is indicative of a rigid and compact structure where the structured segments of the protein tumble together in solution.
Regions that have low heteronuclear NOE values include H3 and adjacent loops (residues 50–78), the Ca2+-binding loop of EF-hand III (residues 99–109), as well as the C-terminal H9 (residues 159–170) (Fig. 3B and 3G).
Protein: DP01311 (UniProt Q6NUK1)
Region: residues 68	to 79
Annotation: calcium ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The crystal structure of the Ca2-bound NTD shows a rigid and elongated architecture that contains three main structured regions: the N-terminal lobe (residues 22–87) and the C-terminal lobe (residues 88–152), each consisting of two Ca2+-bound EF hands, and a C-terminal helix (residues 159–170) (Fig. 1A).
The supplementary Figure S2 shows this region, define as EF-hand II, coordinates Ca+2 ion.
Cross-references: PDB:4N5X
Protein: DP01312 (UniProt Q9UMX1)
Region: residues 279	to 360
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Topology scheme, with the intrinsically disordered region (IDR) represented by a dashed line.
Although the crystallized protein was intact (Supplementary Fig. S2a), both SUFU molecules in the orthorhombic asymmetric unit show no apparent density for the C-terminal domain residues 279–360, suggesting that this region of the molecule is highly mobile.
Collectively, these data suggest that residues 279–360 constitute an intrinsically disordered region (IDR) that is an inherent feature of native human SUFU.
Cross-references: PDB:4BL8
Protein: DP01313 (UniProt Q9N4U5)
Region: residues 163	to 223
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
These observations suggest that ceRED163−223 is unstructured in isolation and that its ceSmu1NTR-interacting α helices are induced upon complex formation
Protein: DP01313 (UniProt Q9N4U5)
Region: residues 163	to 223
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
These observations suggest that ceRED163−223 is unstructured in isolation and that its ceSmu1NTR-interacting α helices are induced upon complex formation
Protein: DP01313 (UniProt Q9N4U5)
Region: residues 163	to 223
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
These observations suggest that ceRED163−223 is unstructured in isolation and that its ceSmu1NTR-interacting α helices are induced upon complex formation
Cross-references: IntAct:EBI-2415311
IntAct:EBI-2411547
Protein: DP01315 (UniProt Q9QWH1)
Region: residues 1	to 79
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
e found that PHC21–79 is disordered in solution as judged by poor peak dispersion on the 1H–15N HSQC spectra (Supplementary Fig. 3).
Protein: DP01315 (UniProt Q9QWH1)
Region: residues 1	to 79
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We found that the most significantly perturbed signals correspond to PHC2 residues 33–59 indicating that this represents the BMI1-binding motif in the PHC2 (Fig. 1f).
Cross-references: IntAct:EBI-927401
Protein: DP01316 (UniProt P25916)
Region: residues 106	to 240
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We assigned disordered fragments in BMI1106-240 by employing a combination of 13C-detected 2D CACO, CBCACO and CANCO experiments using a previously published protocol
Protein: DP01317 (UniProt O60741)
Region: residues 1	to 93
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Density for N-terminal residues 1 to 93 was not visible because these residues are most likely unstructured and disordered (nearly 30% are glycines).
Cross-references: EMDB:EMD-8511
PDB:5U6O
PDB:5U6P
EMDB:EMD-8512
Protein: DP01319 (UniProt Q15796)
Region: residues 241	to 264
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 24 residues are disordered in the crystals.
The N-terminal 24 residues are disordered in the crystals correspond to the UniProt region 241-264.
Cross-references: PDB:1KHX
Protein: DP01319 (UniProt Q15796)
Region: residues 457	to 467
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final refined model contains two complexes of Smad2 (residues 263–456) and SARA (residues 669–709), and 243 water molecules. The NH2- and COOH-terminal residues in Smad2 have no electron density, and we presume that these regions are disordered in the crystals.