LiteFold/DisProt huggingface dataset:
Protein: DP00385 (UniProt P49841)
Region: residues 386	to 420
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several sections of the structure lacked interpretable electron density,
indicating a high degree of disorder. These include
the N-terminal segment 1–34, the loop 120–124
and the C-terminal segment 386–420. In addition,
the electron density was weak for the region 285–
295.
Cross-references: PDB:1Q41
Protein: DP00385 (UniProt P49841)
Region: residues 285	to 300
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the PDB structure of GSK-3 in complex with A inhibitor 13, indicating it is disordered.
Cross-references: PDB:8DJC
Protein: DP00385 (UniProt P49841)
Region: residues 12	to 16
Annotation: palmitoylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
We identified palmitoylation of GSK3β using ABE and
found that both the GSK3β mutant (cysteine 14 mutated to
alanine) and the siRNA silencing of ZDHHC4 made GSK3β
palmitoylation significantly reduced in SF126 GBM cells, similar
to the U118MG cell line (Fig. 1E; Supplementary Fig. 1B, C).
Here, we found that GSK3β was noted as a substrate for ZDHHC4-mediated palmitoylation at the Cys14
residue, which enhanced GBM temozolomide (TMZ) resistance and GSC self-renewal.
Protein: DP00385 (UniProt P49841)
Region: residues 285	to 300
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The binding of FRATtide causes a change in the position of residues 286–296 of GSK-3. In crystal form A (without FRATtide), residues 286–296 pack close to and partially cover phenylalanine 229 and the hydrophobic surface of helix G (the 286–296 loop has high temperature factors in crystal form A, suggesting that the packing of Phe 291, Phe 293, and other residues against helix G is not optimal). Upon binding, FRATtide residues 288–294 of GSK-3 move approximately 6 Å away from helix G and open up a hydrophobic groove, between helix G and the 288–294 loop.
Although this region seems to be disordered when the protein is in complex with an inhibitor, when in complex with a peptide derived from the Proto-oncogene FRAT1, it is structured.
Cross-references: PDB:1GNG
Protein: DP00385 (UniProt P49841)
Region: residues 19	to 23
Annotation: phosphorylation display site (Disorder function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
We demonstrate that serine 21 in GSK-3α and serine 9 in GSK-3β are also physiological substrates of cAMP-dependent protein kinase A (PKA).
Protein: DP00385 (UniProt P49841)
Region: residues 3	to 12
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
To understand the mechanism of PKB regulation, we determined the crystal structures of activated kinase domains of PKB in complex with a GSK3beta-peptide substrate and an ATP analog.
The crystals were grown at 20 °C by
mixing the protein solution (10 mg ml–1 PKB, 5 mM AMPPNP–
MnCl2 and 0.6 mM GSK3β-peptide (GRPRTTSFAE)) with a
crystallization solution of 20% (w/v) PEG 4000, 10% (v/v) isopropanol,
0.1 M HEPES, pH 7.5 and 5 mM dithiothreitol in a micro
batch under oil.
Cross-references: PDB:1O6L
Protein: DP00385 (UniProt P49841)
Region: residues 285	to 299
Annotation: protein binding (Molecular function)
Evidence: crystallography evidence used in manual assertion
Supporting statements:
The crystal structures of apo GSK-3β (crystal form A) and of GSK-3β complexed with the 39mer peptide FRATtide and a sulphate ion (crystal form FS) were determined and refined to 2.9 Å and 2.6 Å, respectively (see Experimental Procedures for details).
The binding of FRATtide causes a change in the position of residues 286–296 of GSK-3. In crystal form A (without FRATtide), residues 286–296 pack close to and partially cover phenylalanine 229 and the hydrophobic surface of helix G (the 286–296 loop has high temperature factors in crystal form A, suggesting that the packing of Phe 291, Phe 293, and other residues against helix G is not optimal). Upon binding, FRATtide residues 288–294 of GSK-3 move approximately 6 Å away from helix G and open up a hydrophobic groove, between helix G and the 288–294 loop.
Cross-references: PDB:1GNG
Protein: DP00385 (UniProt P49841)
Region: residues 7	to 11
Annotation: phosphorylation display site (Disorder function)
Evidence: in vitro protein kinase assay evidence used in manual assertion
Supporting statements:
We demonstrate that serine 21 in GSK-3α and serine 9 in GSK-3β are also physiological substrates of cAMP-dependent protein kinase A (PKA).
Protein: DP00389 (UniProt P09983)
Region: residues 962	to 1023
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In aqueous solution, the CD spectra of  both HlyA and LktA reflect a predominantly  random conformation (Figures 6 and 7). There is no observed structural change between 23 and 37 “C. A broad range of pH changes (pH 4.5-8) do not affect the structure of  either HlyA or LktA signal  peptide.
The C-terminal signal peptides of HlyA and LktA exhibit similar biophysical behaviors. In aqueous solution, both molecules are mainly in a random conformation.
Protein: DP00389 (UniProt P09983)
Region: residues 962	to 1023
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Signal peptides were labelled with 15N to facilitate the NMR analysis. A striking feature of the NMR spectra of both is the poor dispersion in the 1H nuclei, possibly indicating the presence of a significant amount of random-coil or unfolded protein conformation [27]. The 15N-nuclei, on the other hand, have reasonable chemical shift dispersion as has been shown previously for
this nucleus in unfolded proteins [28,29].
The NMR evidence for the helices in HIyA is not as strong as for LktA, presumably due to instability of the helices. Residues 1-34, 47-56 and 68-83 have for the most part random coil Halpha chemical shifts, 3J(NH-Halpha) values between 6-8 Hz and only short-range sequential NOEs (i, i+1 and i, i+2).
Protein: DP00389 (UniProt P09983)
Region: residues 962	to 1023
Annotation: localization (Biological process)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
In order to test the secretion of these signal peptides, C-HA61 or C-LA70 were coexpressed with the transporter proteins HlyB and HlyD in JM83 cells. Cell media were taken at different points during the growth curve. The secreted signal peptides can be detected by Western blot
analysis using C494 antibody. As shown in Figure 3 lanes 3, 4, 7, and 8, signal sequence peptides of HlyA and LktA were found in the medium. This secretion requires the
presence of both HlyB and HlyD.
Thus, these data show that the signal sequence bearing peptides can be transported by the HlyB/D transporter in a specific manner.
This confirms that these short sequences contain information sufficient for recognition and transport, and that no other sequences are required.
Protein: DP00389 (UniProt P09983)
Region: residues 962	to 1023
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Finally, we tested the conformational behaviors of HlyA and LktA signal peptides in phospholipid vesicles, a lipid bilayer environment which more closely resembles a membrane compared to the other reagents tested. Uncharged phospholipids PC could not induce an ordered structure (Figure 7G,H), while the anionic phospholipids (PS, PG) induced formation of a-helices in both peptides (Figure 7C- F).
In aqueous solution, both molecules are mainly in a random conformation. Membrane
mimetic environments such as TFE/H20, SDS micelles, and negatively charged phospholipid vesicles induce formation of a-helices.
Protein: DP00389 (UniProt P09983)
Region: residues 962	to 1023
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Finally, we tested the conformational behaviors of HlyA and LktA signal peptides in phospholipid vesicles, a lipid bilayer environment which more closely resembles a membrane compared to the other reagents tested. Uncharged phospholipids PC could not induce an ordered structure (Figure 7G,H), while the anionic phospholipids (PS, PG) induced formation of a-helices in both peptides (Figure 7C- F).
Protein: DP00395 (UniProt P40136)
Region: residues 580	to 590
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Switch B (578–591), which lies between switch C and the nucleotide substrate, becomes disordered when CaM is not present. This disorder cannot be attributed to the lack of substrate in the EF-alone structure, because switch B is clearly visible in the structure of substrate-free EF–CaM (Fig. 4).
In addition to the helical domain movement, three segments designated as switch A, B and C undergo large conformational changes in response to CaM binding, leaving the remaining residues relatively unchanged (Figs 1 and 4).
In the EF-alone structure switch B is disordered, but it becomes highly ordered in the EF–CaM complex (Fig. 4).
Although Switch B corresponds to region 578-591, only a smaller part of it is disordered and it corresponds to region 580-590 as also shown in PDB:1K8T
Cross-references: PDB:1K8T
Protein: DP00395 (UniProt P40136)
Region: residues 580	to 590
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Switch B (578–591), which lies between switch C and the nucleotide substrate, becomes disordered when CaM is not present. This disorder cannot be attributed to the lack of substrate in the EF-alone structure, because switch B is clearly visible in the structure of substrate-free EF–CaM (Fig. 4).
In addition to the helical domain movement, three segments designated as switch A, B and C undergo large conformational changes in response to CaM binding, leaving the remaining residues relatively unchanged (Figs 1 and 4).
In the EF-alone structure switch B is disordered, but it becomes highly ordered in the EF–CaM complex (Fig. 4). This transition is most probably caused by extensive contacts between switch B and the N-terminal portion of switch C. Notably, Asn 639 forms a hydrogen bond with the main-chain carbonyl of Pro 587. Mutation of Asn 639 to alanine results in a 12-fold reduction in the rate of catalysis (Fig. 4c and Table 1). Thus, we propose that the ordering of switch B occurs as a consequence of the CaM-induced movement of switch C.
On calmodulin binding, an oedema factor helical domain of relative molecular mass 15,000 undergoes a 15 Å translation and a 30° rotation away from the oedema factor catalytic core, which stabilizes a disordered loop and leads to enzyme activation.
Although Switch B corresponds to region 578-591, only a smaller part of it is disordered and it corresponds to region 580-590 as also shown in PDB:1K8T
Cross-references: PDB:1K90
PDB:1K93
Protein: DP00395 (UniProt P40136)
Region: residues 580	to 590
Annotation: dATP binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Switch B (residues 579–591) contains several residues that either bind ATP directly or stabilize the catalytic residues (Fig. 3).
Phe 586 and Leu 348 lie above and below the plane of the ribose, and the side chain of Asn 583 forms a hydrogen bond with O4′ of the ribose ring. The adenosine ring, although solvent accessible, contacts the backbone of Asp 582 and Asn 583, and the N6 nitrogen is within hydrogen-bonding distance of the main-chain carbonyls of Thr 579 and Thr 548.
Cross-references: PDB:1K90
Protein: DP00396 (UniProt O74718)
Region: residues 196	to 214
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In all three structures, three regions of polypeptide are not visible in the electron density map and are assumed to be disordered, namely residues 196-214, 280-307, and 325-335.
Cross-references: PDB:1R5B
Protein: DP00396 (UniProt O74718)
Region: residues 280	to 307
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In all three structures, three regions of polypeptide are not visible in the electron density map and are assumed to be disordered, namely residues 196-214, 280-307, and 325-335.
Cross-references: PDB:1R5B
Protein: DP00396 (UniProt O74718)
Region: residues 325	to 335
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In all three structures, three regions of polypeptide are not visible in the electron density map and are assumed to be disordered, namely residues 196-214, 280-307, and 325-335.
Cross-references: PDB:1R5B
Protein: DP00396 (UniProt O74718)
Region: residues 301	to 305
Annotation: magnesium ion binding (Molecular function)
Evidence: curator inference used in manual assertion
Supporting statements:
The rest of switch I in eRF3c, which contains the conserved metal binding residue Thr303 (Thr61 of EF-Tu), is disordered.
Protein: DP00399 (UniProt P50097)
Region: residues 102	to 221
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The smaller domain, residues 102−220, is not visible in the electron density maps, presumably due to disorder.
Cross-references: PDB:1AK5
Protein: DP00399 (UniProt P50097)
Region: residues 314	to 327
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Other disordered segments of the IMPDH structure include three flexible loops formed by residues 314−324 (between strand 6 and helix 6 of the barrel), 413−431 (following helix 8 of the barrel), and 484−503 (the C terminus).
Cross-references: PDB:1AK5
Protein: DP00399 (UniProt P50097)
Region: residues 413	to 431
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Other disordered segments of the IMPDH structure include three flexible loops formed by residues 314−324 (between strand 6 and helix 6 of the barrel), 413−431 (following helix 8 of the barrel), and 484−503 (the C terminus).
Cross-references: PDB:1AK5
Protein: DP00399 (UniProt P50097)
Region: residues 484	to 503
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Other disordered segments of the IMPDH structure include three flexible loops formed by residues 314−324 (between strand 6 and helix 6 of the barrel), 413−431 (following helix 8 of the barrel), and 484−503 (the C terminus).
Cross-references: PDB:1AK5
Protein: DP00407 (UniProt P07363)
Region: residues 124	to 158
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR experiments were conducted on a 139 amino acid fragment of CheA which contains the 69 residue CheY-binding domain (residues 159−227) as well as two unstructured domain linkers (residues 124−158 and 228−257).
Cross-references: PDB:1FWP
Protein: DP00407 (UniProt P07363)
Region: residues 124	to 158
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR experiments were conducted on a 139 amino acid fragment of CheA which contains the 69 residue CheY-binding domain (residues 159−227) as well as two unstructured domain linkers (residues 124−158 and 228−257).
Protein: DP00407 (UniProt P07363)
Region: residues 228	to 257
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR experiments were conducted on a 139 amino acid fragment of CheA which contains the 69 residue CheY-binding domain (residues 159−227) as well as two unstructured domain linkers (residues 124−158 and 228−257).
Cross-references: PDB:1FWP
Protein: DP00407 (UniProt P07363)
Region: residues 228	to 257
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR experiments were conducted on a 139 amino acid fragment of CheA which contains the 69 residue CheY-binding domain (residues 159−227) as well as two unstructured domain linkers (residues 124−158 and 228−257).
Protein: DP00410 (UniProt P12497)
Region: residues 354	to 363
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues 222−231 at the carboxy terminus are disordered.
Region 222-231 described in the publication corresponds to the 354-363 residues of the Gag-Pol polyprotein.
Cross-references: PDB:2JYG
PDB:2JYL
Protein: DP00410 (UniProt P12497)
Region: residues 351	to 377
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks of electron density in the PDB, indicating disorder. The peptide assessed in this publication is derived from the HIV-1 isolate NL4-3, however the IDR is 100% identical to this Uniprot.
Cross-references: PDB:1BAJ
Protein: DP00410 (UniProt P12497)
Region: residues 108	to 143
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure indicates that Gag1-278 comprises ordered MA and CAN domains that are connected by a flexible linker (Figure 1a and b). 
The last 25 residues of the Gag1-278 MA domain and the first 10 residues of the CAN domain are disordered and have been omitted from the refined model of Gag1-278. This flexibility for residues 108−143 could easily accommodate the ∼40 Å gap between the MA and CAN domains that has been inferred for immature virions from electron microscopy ( 12).
Cross-references: PDB:2GOL
Protein: DP00410 (UniProt P12497)
Region: residues 108	to 143
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The last 25 residues of the Gag1-278 MA domain and the first 10 residues of the CAN domain are disordered and have been omitted from the refined model of Gag1-278. This flexibility for residues 108−143 could easily accommodate the ∼40 Å gap between the MA and CAN domains that has been inferred for immature virions from electron microscopy ( 12).
Cross-references: PDB:2GOL
PDB:2GON
Protein: DP00410 (UniProt P12497)
Region: residues 123	to 143
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues Gly 2–Ser 6, Gly 123–Val 143 and Pro 279–Leu 283 show relatively low {1H}-15N heteronuclear NOE (XNOE) and T2 relaxation values (Fig. 2), as well as few or no medium-range 1H-1H NOEs, indicating that these residues are conformationally labile. 
Because no restraints were used for the mobile residues that connect the folded domains (Gly 123–Val 143) and no NOEs were observed between the domains, the relative orientation of the MA and CAN domains is not defined.
Cross-references: PDB:1L6N
Protein: DP00410 (UniProt P12497)
Region: residues 123	to 143
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues Gly 2–Ser 6, Gly 123–Val 143 and Pro 279–Leu 283 show relatively low {1H}-15N heteronuclear NOE (XNOE) and T2 relaxation values (Fig. 2), as well as few or no medium-range 1H-1H NOEs, indicating that these residues are conformationally labile. 
Because no restraints were used for the mobile residues that connect the folded domains (Gly 123–Val 143) and no NOEs were observed between the domains, the relative orientation of the MA and CAN domains is not defined.
Cross-references: PDB:1L6N
BMRB:5316
Protein: DP00410 (UniProt P12497)
Region: residues 217	to 231
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Residues Pro 217–Pro 231, which include the CypA-binding site, form a conformationally flexible loop.
Cross-references: PDB:1L6N
PDB:1GWP
BMRB:5316
Protein: DP00410 (UniProt P12497)
Region: residues 133	to 143
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, the conformation of residues Pro 133–Val 143 of Gag283 is substantially different from that observed in the mature CAN protein. No intermediate or long-range 1H-1H NOEs were observed for these residues in Gag283, and the chemical shift index data indicate that they exist in a random coil conformation (Fig. 2).
The present findings confirm that the β-hairpin is unfolded in the immature protein and support the proposal that β-hairpin formation occurs subsequent to proteolytic cleavage of Gag, triggering capsid assembly4,12. 
Cross-references: PDB:1L6N
BMRB:5316
Protein: DP00410 (UniProt P12497)
Region: residues 352	to 377
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks of electron density in the PDB, indicating disorder. The peptide assessed in this publication is derived from the HIV-1 isolate NL4-3, however the IDR is 100% identical to this Uniprot.
Cross-references: PDB:1A43
PDB:1BAJ
Protein: DP00410 (UniProt P12497)
Region: residues 1288	to 1300
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks of electron density in the PDB, indicating disorder.
Cross-references: PDB:1ITG
Protein: DP00410 (UniProt P12497)
Region: residues 1193	to 1202
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Four copies of both the NTD and the CCD were present in the asymmetric unit (Fig. 1a), with the inter-domain linker (residues 47–55) unresolved in the electron density.
Authors are referring to the 1193-1202 region of the Gag-Pol polyprotein that, as shown in the PDB, is disordered. 
Cross-references: PDB:6VRG
Protein: DP00410 (UniProt P12497)
Region: residues 1286	to 1295
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating disorder, as shown in the PDB.
Cross-references: PDB:6VRG