LiteFold/DisProt huggingface dataset:
Protein: DP02757 (UniProt Q9GZU1)
Region: residues 564	to 568
Annotation: palmitoylation display site (Disorder function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
We have also found that the C-terminal tail of mucolipin-1 is palmitoylated and that this modification might regulate the efficiency of endocytosis. Finally, the mutagenesis of both di-leucine motifs abrogated lysosomal accumulation and resulted in cell-surface redistribution of mucolipin-1. Taken together, these results reveal novel information regarding the motifs that regulate mucolipin-1 trafficking and suggest a role for palmitoylation in protein sorting.
Palmitoylation mediates the association of the C-terminal tail of mucolipin-1 with membranes
These data suggest that the C565CC sequence is required for palmitoylation and subsequent association with membranes although the acidic di-leucine motif mediates localization at endosomes.
Together, our results suggest that the palmitoylation of the C-terminal tail of mucolipin-1 may play a role in regulating its trafficking possibly through bringing the endocytic signal closer to the plasma membrane, thus increasing the efficiency of endocytosis.
Therefore, we conclude that mucolipin-1 is palmitoylated in vivo and that Cys565, Cys566 and Cys567 account for the total palmitoylation of the protein.
Protein: DP02757 (UniProt Q9GZU1)
Region: residues 48	to 59
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The apo TRPML1 at pH 7.0 was determined at 3.7 Å, representing a closed conformation; the ML-SA1-bound TRPML1 at pH 6.0 was determined at 3.5 Å, representing an open conformation (Extended Data Figs 2b, ​,33 and Extended Data Table 1).
The electron density is clearly resolved for residues 60–526 in the apo TRPML1 and residues 38–526 in the ML-SA1-bound TRPML1 (Extended Data Fig. 4), with the exception of a short linker in the luminal domain (amino acids 206–215).
Cross-references: PDB:5WJ9
Protein: DP02758 (UniProt Q13563)
Region: residues 198	to 215
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
At 3.0 Å resolution, the cryo-EM map was of sufficient quality for de novo atomic model building in Coot (Emsley et al., 2010) except for the disordered N terminus (198–215), a loop (296–301) within the extracellular polycystin domain, S2–S3 loop (494–503), and C terminus (695–703).
Cross-references: PDB:5T4D
Protein: DP02758 (UniProt Q13563)
Region: residues 494	to 503
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
At 3.0 Å resolution, the cryo-EM map was of sufficient quality for de novo atomic model building in Coot (Emsley et al., 2010) except for the disordered N terminus (198–215), a loop (296–301) within the extracellular polycystin domain, S2–S3 loop (494–503), and C terminus (695–703).
Cross-references: PDB:5T4D
Protein: DP02759 (UniProt Q14181)
Region: residues 1	to 156
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Both the NTD and an extended linker (residues 79–156) between the NTD and the PDE are not visible in crystal formation, pointing to the absence of stabilizing interactions with the PDE, the OB, and p180C. The only exception is molecule 2 residues 151–156 that are stabilized by interactions with the neighboring molecule
Cross-references: PDB:4Y97
Protein: DP02759 (UniProt Q14181)
Region: residues 79	to 156
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal domain and the linker connecting it to the PDE domain are disordered in the reported crystal structure. 
Both the NTD and an extended linker (residues 79–156) between the NTD and the PDE are not visible in crystal formation, pointing to the absence of stabilizing interactions with the PDE, the OB, and p180C. The only exception is molecule 2 residues 151–156 that are stabilized by interactions with the neighboring molecule
In Prim-Pol α, the CTD-B subunit complex plays an additional and unique role by tethering two catalytic domains and regulating their activities (53).
Cross-references: PDB:4Y97
Protein: DP02760 (UniProt P76216)
Region: residues 19	to 34
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The only significant difference between the molecules is the conformation of a loop, Ala19–Gln34, which is largely disordered in the apo protein but becomes well ordered in the presence of bound substrate or product.
Cross-references: PDB:1YNF
Protein: DP02760 (UniProt P76216)
Region: residues 19	to 34
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Like other members of the AT superfamily of enzymes, AstB possesses a flexible loop that is disordered in the absence of substrate and assumes an ordered conformation upon substrate binding, shielding the ligand from the bulk solvent, thereby controlling substrate access and product release.
The only significant difference between the molecules is the conformation of a loop, Ala19–Gln34, which is largely disordered in the apo protein but becomes well ordered in the presence of bound substrate or product.
An electron density map calculated from diffraction data collected from this crystal revealed a well defined substrate molecule bound in the active site (Fig. 3a). As a result of substrate binding, all of the residues in the Ala19–Arg32 loop, which were disordered in the native crystal structures, were now clearly defined in electron density.
Cross-references: PDB:1YNI
PDB:1YNH
PDB:1YNF
Protein: DP02760 (UniProt P76216)
Region: residues 19	to 34
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
An electron density map calculated from diffraction data collected from this crystal revealed a well defined substrate molecule bound in the active site (Fig. 3a). As a result of substrate binding, all of the residues in the Ala19–Arg32 loop, which were disordered in the native crystal structures, were now clearly defined in electron density.
Cross-references: PDB:1YNI
PDB:1YNH
Protein: DP02761 (UniProt P25299)
Region: residues 127	to 232
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
By CD spectroscopy, each of these isolated peptides is minimally folded (Figure 1B), with only minor indication of a thermal denaturation unfolding transition for His6-Rna15p(127–232). NMR spectroscopy data are also consistent with peptides that are either unfolded or in a heterogeneous molten-globule state (Figure 1C). This is evident by the poor dispersion in the 1H chemical shift values as is seen with disordered peptides
Cross-references: PDB:2L9B
Protein: DP02761 (UniProt P25299)
Region: residues 127	to 232
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
By CD spectroscopy, each of these isolated peptides is minimally folded (Figure 1B), with only minor indication of a thermal denaturation unfolding transition for His6-Rna15p(127–232). NMR spectroscopy data are also consistent with peptides that are either unfolded or in a heterogeneous molten-globule state (Figure 1C). This is evident by the poor dispersion in the 1H chemical shift values as is seen with disordered peptides
Cross-references: PDB:2L9B
Protein: DP02761 (UniProt P25299)
Region: residues 127	to 232
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The C-terminal monkeytail domain from Rna14p and the hinge region from Rna15p display a coupled binding and folding mechanism, where both peptides are initially disordered. 
Excellent stability and evidence of a single well-folded complex by nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy is seen with samples from bacterially coexpressed Rna14p(626–677)/Rna15p(127–232)
The authors show that while the individual Rna15p and Rna14p proteins are disordered and show low NMR dispersion, the co-expressed complex is folded and has a highly dispersed spectrum (Figure 1C)
Cross-references: PDB:2L9B
Protein: DP02761 (UniProt P25299)
Region: residues 127	to 232
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Excellent stability and evidence of a single well-folded complex by nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy is seen with samples from bacterially coexpressed Rna14p(626–677)/Rna15p(127–232)
The authors show that while the individual Rna15p and Rna14p proteins are disordered and show low NMR dispersion, the co-expressed complex is folded and has a highly dispersed spectrum (Figure 1C)
Genetic data confirm that mutation of residues within the minimal heterodimer region inhibit association of full-length Rna14p and Rna15p.
Cross-references: PDB:2L9B
Protein: DP02761 (UniProt P25299)
Region: residues 127	to 232
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Mutants with destabilized monkeytail-hinge interactions prevent association of Rna15p within CF IA. Conservation of interdomain residues reveals that the structural tethering is preserved in the homologous mammalian ... proteins of the CstF complex.
The interaction between the monkeytail and hinge domains creates a high affinity link that joins Rna14p and Rna15p together in a tight complex, and from sequence analysis a similar tether is likely formed between the metazoan orthologs
Using TAP-tag purification we have found that the loss of this tether specifically results in a separation of Rna15p from CF IA.
Most importantly, without Rna15p the RRM domain is no longer present in the CF IA complex, causing loss of specific RNA-binding for CF IA, even though the RRM domain itself is not directly affected by either mutation.
Cross-references: PDB:2L9B
Protein: DP02763 (UniProt Q9VI75)
Region: residues 4	to 21
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As the residues in segments at the N-terminal end (4–21) and in two long loops (117–119 and 163–166) and the last two residues have weak or uninterpretable densities, they were assumed to be flexible.
The crystal structure of the NAP domain (residues 4–301) was determined by the multiple anomalous dispersion (MAD) phasing technique (Experimental Procedures and Table 1) . The structure, missing the first eighteen disordered residues, is composed entirely of ten α helices and connecting loops, all of varying lengths.
Cross-references: PDB:1HX8
Protein: DP02764 (UniProt Q13162)
Region: residues 1	to 75
Annotation: molecular adaptor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, in the full-length Prx4 structure, the N-terminal 1–37 residues were invisible (which was not due to degradation; results not shown) and residues 38–46 adopt an unwound loop. Thus this region was proposed to be flexible and exposed to the solvent.
In contrast, oxidized Prx4 exists in a rather stable decameric form, probably stabilized by its unique flexible N-terminal region.
The mutant Prx4-ΔN, lacking the N-terminal 46 residues, was predominantly a decamer in a reduced state, but partially dissociated into dimers especially at lower concentrations after reaction with H2O2, suggesting that the flexible N-terminal region may play a role in stabilization of the Prx4 decamer in the oxidized state.
Cross-references: PDB:3TKQ
PDB:3TKP
PDB:3TKS
PDB:3TKR
Protein: DP02764 (UniProt Q13162)
Region: residues 1	to 75
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, in the full-length Prx4 structure, the N-terminal 1–37 residues were invisible (which was not due to degradation; results not shown) and residues 38–46 adopt an unwound loop. Thus this region was proposed to be flexible and exposed to the solvent.
In contrast, oxidized Prx4 exists in a rather stable decameric form, probably stabilized by its unique flexible N-terminal region.
Cross-references: PDB:3TKQ
PDB:3TKP
PDB:3TKS
PDB:3TKR
Protein: DP02764 (UniProt Q13162)
Region: residues 1	to 271
Annotation: molecular sequestering activity (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
The second-order rate constant for the reaction of Prx4 with H2O2 was determined to be 2.2 × 107 M−1·s−1 (Figure 6A), indicating that Prx4 can remove H2O2 as efficiently as haem or selenium peroxidases and other Prxs do.
The peroxidase activity was also monitored in a reaction coupled to NADPH oxidation (Figure 6B). NADPH was oxidized with an initial reaction rate of ~1 μM·s−1 in the presence of 2.5 μM Prx4 and 50 μM H2O2, the minimal amount for quantitatively monitoring the reaction in practice. When the H2O2 concentrations increased, the oxidation rate of NADPH decreased, indicating loss of peroxidase activity of Prx4.
Overoxidation of wild-type Prx4 intensified with increasing H2O2 concentrations, whereas the overoxidation of Prx4-ΔC and Prx4-T118E remained negligible, with a faint increase only at 500 μM H2O2.
Prx4 (peroxiredoxin 4) is the only peroxiredoxin located in the ER (endoplasmic reticulum) and a proposed scavenger for H2O2. In the present study, we solved crystal structures of human Prx4 in three different redox forms and characterized the reaction features of Prx4 with H2O2.
Protein: DP02765 (UniProt Q14118)
Region: residues 163	to 179
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Upon completion of the crystallographic refinement, the final R‐factor was 0.163 (R‐free = 0.195), with residues 52–60, 163–179, and 305–315 missing in the final model as no reliable electron density could be detected for these regions.
Cross-references: PDB:5LLK
Protein: DP02765 (UniProt Q14118)
Region: residues 163	to 179
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Upon completion of the crystallographic refinement, the final R‐factor was 0.163 (R‐free = 0.195), with residues 52–60, 163–179, and 305–315 missing in the final model as no reliable electron density could be detected for these regions.
The hα‐DG‐Nt and mα‐DG‐Nt crystal structures display the most significant structural differences in the flexible linker (see Fig. S2A,B) connecting the Ig‐like and S6 domains.
Cross-references: PDB:5LLK
Protein: DP02765 (UniProt Q14118)
Region: residues 305	to 315
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Upon completion of the crystallographic refinement, the final R‐factor was 0.163 (R‐free = 0.195), with residues 52–60, 163–179, and 305–315 missing in the final model as no reliable electron density could be detected for these regions.
Cross-references: PDB:5LLK
Protein: DP02765 (UniProt Q14118)
Region: residues 163	to 179
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Rg distributions of these ensembles (Fig. 7, solid lines) are very similar to each other and nearly as broad as the distribution of randomly generated models (Fig. 7, dashed lines), supporting the hypothesis of a certain degree of interdomain flexibility.
Protein: DP02765 (UniProt Q14118)
Region: residues 163	to 179
Annotation: flexible linker (Disorder function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The Rg distributions of these ensembles (Fig. 7, solid lines) are very similar to each other and nearly as broad as the distribution of randomly generated models (Fig. 7, dashed lines), supporting the hypothesis of a certain degree of interdomain flexibility.
Protein: DP02767 (UniProt P15442)
Region: residues 921	to 951
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A segment between αF and αH (residues 921-951) exhibits high B-factors, consistent with disorder.
Protein: DP02767 (UniProt P15442)
Region: residues 861	to 882
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Approximately 22 residues at the center of the activation loop (residues 861-882) appear disordered and are invisible in experimental electron density maps (Figs. 1b and 2a). 
Cross-references: PDB:1ZYD
PDB:1ZYC
PDB:1ZY5
PDB:1ZY4
PDB:1ZXE
Protein: DP02767 (UniProt P15442)
Region: residues 861	to 882
Annotation: phosphorylation display site (Disorder function)
Evidence: protein kinase assay evidence used in manual assertion
Supporting statements:
Approximately 22 residues at the center of the activation loop (residues 861-882) appear disordered and are invisible in experimental electron density maps (Figs. 1b and 2a). 
Autophosphorylation sites within the activation segment, Thr887 and Thr882 (42), are not phosphorylated in any of the purified proteins used for crystallization
The activating mutations R794G and F842L lead to increased autophosphorylation of the GCN2 activation loop (Fig. 4a), and there is genetic evidence that phosphorylation of both Thr887 and Thr882 in this loop is required for full activity even in the presence of these GCN2c mutations
Subsequent autophosphorylation of the activation loop is predicted to facilitate an additional realignment of active site residues necessary for substrate phosphorylation.
Protein: DP02767 (UniProt P15442)
Region: residues 1519	to 1537
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The mCTD structural model includes residues 1530–1648 for the A chain and 1526–1648 for the B chain; the yCTD includes residues 1537–1549 and 1559–1659 for the A chain and residues 1538–1555 and 1560–1659 for the B chain. Missing residues in yCTD are disordered and correspond to the connecting loop region between the N-terminal β-strand and α-helix.
Cross-references: PDB:4OTM
Protein: DP02767 (UniProt P15442)
Region: residues 1519	to 1537
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The mCTD structural model includes residues 1530–1648 for the A chain and 1526–1648 for the B chain; the yCTD includes residues 1537–1549 and 1559–1659 for the A chain and residues 1538–1555 and 1560–1659 for the B chain. Missing residues in yCTD are disordered and correspond to the connecting loop region between the N-terminal β-strand and α-helix.
Cross-references: PDB:4OTM
Protein: DP02767 (UniProt P15442)
Region: residues 665	to 767
Annotation: disorder (Structural state)
Evidence: in vitro cleavage assay evidence used in manual assertion
Supporting statements:
The GCN2 fragment (from S. cerevisiae) encompassing residues 594-997 with deleted segment 665-767, and the same fragments bearing the D835N or R794G mutations, were expressed in Escherichia coli BL21(DE3*) cells as N-terminal His6-Smt3 fusion proteins (26) using a pET26b-derived expression vector (both S- and Se-methionine forms).
Limited proteolysis/mass spectrometry studies of the GCN2 PK domain (residues 593-998) confirmed the presence of a large (102 residue) proteolytically sensitive insert that is poorly conserved among GCN2 homologs (Fig. 1b).
Protein: DP02768 (UniProt P09950)
Region: residues 58	to 71
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The variant used for crystallization lacked the mitochondrial targeting sequence (residues 1–57, (Vogtle et al., 2009)), and the first 13 residues of the mature N-terminus were disordered in the final refined structure.
Cross-references: PDB:5TXT
PDB:5TXR
Protein: DP02768 (UniProt P09950)
Region: residues 83	to 113
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
NT (near the mature N-terminus, residues 83–113) was only ordered in subunit B. NTB includes part of helix α1, an extended loop, strand β1, and the loop leading to β2.
Cross-references: PDB:5TXT
Protein: DP02768 (UniProt P09950)
Region: residues 83	to 113
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
NT (near the mature N-terminus, residues 83–113) was only ordered in subunit B. NTB includes part of helix α1, an extended loop, strand β1, and the loop leading to β2.
PLP binding is coupled to disorder-order transitions in three distinct regions of ALAS
Cross-references: PDB:5TXT
PDB:5TXR
Protein: DP02768 (UniProt P09950)
Region: residues 147	to 156
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
GR, which overlaps with a conserved glycine-rich motif (Gong and Ferreira, 1995), by contrast, was ordered only in the A subunit and consists of residues 147–156. The ordered GRA element packs against the PLP cofactor-binding pocket that was in the B subunit.
PLP binding is coupled to disorder-order transitions in three distinct regions of ALAS
Cross-references: PDB:5TXT
PDB:5TXR
Protein: DP02768 (UniProt P09950)
Region: residues 147	to 156
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
GR, which overlaps with a conserved glycine-rich motif (Gong and Ferreira, 1995), by contrast, was ordered only in the A subunit and consists of residues 147–156. The ordered GRA element packs against the PLP cofactor-binding pocket that was in the B subunit.
PLP binding is coupled to disorder-order transitions in three distinct regions of ALAS
Cross-references: PDB:5TXT
PDB:5TXR
Protein: DP02768 (UniProt P09950)
Region: residues 538	to 548
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
CT is comprised of residues 538–548, the last 11 residues of the eukaryote-specific C-terminal extension in ALASSc. The ordered CTA element from the PLP-free subunit also contributed to the assembled active site of the opposite B subunit.
Cross-references: PDB:5TXT
PDB:5TXR