LiteFold/DisProt huggingface dataset:
Protein: DP04235 (UniProt Q03390)
Region: residues 128	to 186
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Binding affinities of Vps60(128–186) for wild-type and mutant Vta1NTD determined by isothermal titration calorimetry assay.
An affinity of Kd=0.7±0.1 μm was measured for the binding of the wild type protein constructs.
Protein: DP04235 (UniProt Q03390)
Region: residues 128	to 186
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
GST or GST-tagged Vps60(128–186) was used to pull down wild-type or mutant Vta1NTD as indicated.
Protein: DP04236 (UniProt Q06263)
Region: residues 65	to 75
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The entire structure can be visualized except for residues 65-75, which are presumed disordered.
Cross-references: PDB:2RKK
Protein: DP04236 (UniProt Q06263)
Region: residues 65	to 75
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the free Vta1NTD structure (29), the linker adopts largely a random coil structure, with only a one-turn α-helix occurring at residues 80–84. In particular, residues 65–75 appear to be disordered in the structure. Upon Vps60 binding, the linker becomes ordered. Residues 68–71 become a one-turn α-helix, and residues 73–84 adopt a longer helical structure (Fig. 2F). This conformational change might be caused by the interactions between helix α4 (positions 73–84) of Vta1NTD and a short N-terminal α-helix (positions 128–134) of Vps60(128–186) (Fig. 2G).
Cross-references: PDB:2LUH
Protein: DP04236 (UniProt Q06263)
Region: residues 65	to 75
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the free Vta1NTD structure (29), the linker adopts largely a random coil structure, with only a one-turn α-helix occurring at residues 80–84. In particular, residues 65–75 appear to be disordered in the structure. Upon Vps60 binding, the linker becomes ordered. Residues 68–71 become a one-turn α-helix, and residues 73–84 adopt a longer helical structure (Fig. 2F). This conformational change might be caused by the interactions between helix α4 (positions 73–84) of Vta1NTD and a short N-terminal α-helix (positions 128–134) of Vps60(128–186) (Fig. 2G).
Cross-references: PDB:2LUH
Protein: DP04236 (UniProt Q06263)
Region: residues 65	to 75
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Binding affinities of Vps60(128–186) for wild-type and mutant Vta1NTD determined by isothermal titration calorimetry assay.
An affinity of Kd=0.7±0.1 μm was measured for the binding of the wild type protein constructs.
Protein: DP04236 (UniProt Q06263)
Region: residues 65	to 75
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
GST or GST-tagged Vps60(128–186) was used to pull down wild-type or mutant Vta1NTD as indicated.
Protein: DP04237 (UniProt Q8N5K1)
Region: residues 57	to 72
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Fifteen amino acids at the N-termini are disordered and not resolved in the electron density.
Cross-references: PDB:3FNV
Protein: DP04239 (UniProt P53355)
Region: residues 303	to 334
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In contrast to the structure of the DAPK1-CaM complex (de Diego et al., 2010), part of the ARD beyond the Ser308 phosphorylation site (residues 303–334) remained invisible, indicating a transient binding of Ser308 to the CD during autophosphorylation (Figure S2).
Cross-references: PDB:2W4K
Protein: DP04239 (UniProt P53355)
Region: residues 303	to 320
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the DAPK(1–334)-CaM complex, the C-terminal portion of the ARD (residues 293 to 320) forms a long seven-turn helix.
In contrast to the apo-structure, the PDB complex structure shows the complete ARD (residues 278–320) to be folded into a α helix, which indicates that the 303-320 region gains order.
Cross-references: PDB:2X0G
Protein: DP04239 (UniProt P53355)
Region: residues 305	to 312
Annotation: calmodulin binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In addition, several ARD residues (Trp305, Ser308, Val309, Ile312) project into well-formed pockets of the CaM C-terminal lobe (Figs. 2A, 3A, and fig. S2). Of these, the deepest and largest cavity is provided by as many as 10 different CaM residues for Trp305. The only side chain–specific interaction involves the DAPK autophosphorylation target Ser308 and CaM residue Glu114.
Cross-references: PDB:2X0G
Protein: DP04239 (UniProt P53355)
Region: residues 303	to 320
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the DAPK(1–334)-CaM complex, the C-terminal portion of the ARD (residues 293 to 320) forms a long seven-turn helix.
In contrast to the apo-structure, the PDB complex structure shows the complete ARD (residues 278–320) to be folded into a α helix, which indicates that the 303-320 region gains order.
Cross-references: PDB:2X0G
Protein: DP04239 (UniProt P53355)
Region: residues 302	to 320
Annotation: calmodulin binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
We characterized the interaction of a synthetic DAPK(ARD) peptide (residues 302 to 320) with CaM by structural and biochemical analysis to determine potential differences in its CaM binding with that of the DAPK(1–334) protein (Fig. 1B, fig. S3, and table S1); the DAPK(ARD) (302–320) peptide-bound CaM with a dissociation constant of 24 nM, forming a high-affinity complex.
Protein: DP04239 (UniProt P53355)
Region: residues 306	to 310
Annotation: phosphorylation display site (Disorder function)
Evidence: qualitative western immunoblotting evidence used in manual assertion
Supporting statements:
Whereas Western blot analysis with phosphospecific antibodies revealed only slight Ser308 phosphorylation of DAPK coexpressed with CaM after adenosine triphosphate (ATP) incubation, we found strong Ser308 phosphorylation of the apoenzyme (Fig. 5C).
Protein: DP04239 (UniProt P53355)
Region: residues 306	to 310
Annotation: negative regulation of kinase activity (Biological process)
Evidence: protein kinase assay evidence used in manual assertion
Supporting statements:
That is, DAPK in complex with CaM, which prevented Ser308 phosphorylation, was as active as the constitutively active DAPK(CD) fragment, whereas the apo version of DAPK(1–334) showed little catalytic activity (Fig. 5B and Table 3).
Autophosphorylation at Ser-308 inhibits its catalytic activity.
Protein: DP04239 (UniProt P53355)
Region: residues 306	to 310
Annotation: self-inhibition (Disorder function)
Evidence: protein kinase assay evidence used in manual assertion
Supporting statements:
That is, DAPK in complex with CaM, which prevented Ser308 phosphorylation, was as active as the constitutively active DAPK(CD) fragment, whereas the apo version of DAPK(1–334) showed little catalytic activity (Fig. 5B and Table 3).
Autophosphorylation at Ser-308 inhibits its catalytic activity.
Protein: DP04240 (UniProt Q8GXC2)
Region: residues 1	to 227
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Figure 1d shows the CD spectra of PHL4effector and PHL4FL. Analysis of the spectra using BeStSel (Micsonai et al., 2022) with the “Disordered-Ordered” classification is summarized in Figure 1e. The prediction for the PHL4effector spectrum is consistent with a disordered protein, while the prediction for PHL4FL is consistent with a mixture of ordered secondary structure motifs accounting for approximately half of the protein.
CD spectra in Figure 1 shows this region is intrinsically disordered because of its large negative ellipticity at 200 nm. PHL4effector is used by the authors to refer to the first 227 N-terminal residues of this protein.
Protein: DP04240 (UniProt Q8GXC2)
Region: residues 1	to 227
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
For PHL4effector, the Rh measured using both SEC and diffusion NMR is consistent with monomeric, unfolded protein.
Protein: DP04240 (UniProt Q8GXC2)
Region: residues 1	to 227
Annotation: disorder (Structural state)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
For PHL4effector, the Rh measured using both SEC and diffusion NMR is consistent with monomeric, unfolded protein.
Protein: DP04240 (UniProt Q8GXC2)
Region: residues 1	to 227
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Large positive values over several adjacent residues indicates an a-helical structure, while large negative values for neighboring residues are consistent with a β-strand structure (Wishart, 2011). These plots show that the majority of the secondary chemical shift magnitudes are less than 2, a commonly used cutoff for well-defined structure (Wishart, 2011). The secondary chemical shifts are therefore consistent with the assigned residues in both PHL4FL and PHL4effector lacking well-defined secondary structure.
Overwhelmingly, random coil is the dominant prediction for PHL4effector, which is consistent with our interpretation for the measured Rh, CD spectra, and Trp fluorescence assays.
Cross-references: BMRB:52525
BMRB:52524
Protein: DP04240 (UniProt Q8GXC2)
Region: residues 369	to 397
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The secondary chemical shifts are therefore consistent with the assigned residues in both PHL4FL and PHL4effector lacking well-defined secondary structure.
At the C-terminus of PHL4FL, in agreement with the secondary chemical shift analysis, the TALOS-N predictions predict a random coil arrangement.
The tetrameric state upper bound is near the value calculated for a completely unfolded PHL4FL, which is compatible with the domain structure of PHL4FL in Figure 1a showing the structured coiled-coil and helix-turn-helix domains occupying only ~28% of the PHL4FL sequence and our solution NMR measurements showing the N- and C-termini are disordered (vide infra).
(a) A domain map for PHL4. HTH DBD is the homology predicted helix-turn-helix DNA binding domain, CC is the homology predicted coiled-coil domain, and residues 1–227 and 369–397 are to be shown in this work as primarily disordered.
Cross-references: BMRB:52524
Protein: DP04241 (UniProt P15146-3)
Region: residues 1	to 467
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The MAP2c is a 49.2 kDa intrinsically disordered protein.
Figure 3 shows the backbone amide resonances of this protein fall between 8.0 and 8.5 p.p.m. The lack of chemical shift dispersion reflect the intrinsic mobility of this protein.
Protein: DP04241 (UniProt P15146-3)
Region: residues 1	to 159
Annotation: protein kinase binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Isothermal titration calorimetry (ITC) of MAP2c and hexahistidine-tagged N-terminal fragment of MAP2c containing residues 1 to 159 (N-MAP2c) titrated by RIIα-PKA and RIIDD2 provided steep-binding isotherms corresponding to the dissociation constants KD in a lower nanomolar range. Similar binding isotherms for MAP2c and N-MAP2c show that the main interaction site of RIIα-PKA is located in the N-terminal part of MAP2c.
Protein: DP04241 (UniProt P15146-3)
Region: residues 80	to 118
Annotation: protein kinase binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The complex with RIIα-PKA exhibited a dramatic decrease in the same region of MAP2c, but a substantial broadening was also observed in other regions, especially in the proline-rich region P2 (residues Ser280–Leu300) and in the microtubule-binding repeat 3 (Val333–Arg363).
In summary, we confirmed that MAP2c binds RIIα-PKA via the residues Thr80–Asp118, in agreement with the literature (24). Interactions with other regions of MAP2c were also observed, but their contribution to the overall binding was weak.
Protein: DP04241 (UniProt P15146-3)
Region: residues 80	to 118
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR peak broadening was used to map the residues of MAP2c influenced by the interactions with RIIα-PKA. Peaks of intrinsically disordered residues of MAP2c are sharp due to its fast motions in spite of its large size. The MAP2c residues interacting with RIIα-PKA become a part of a large, well ordered complex and their peaks broaden dramatically.
In summary, we confirmed that MAP2c binds RIIα-PKA via the residues Thr80–Asp118, in agreement with the literature (24). Interactions with other regions of MAP2c were also observed, but their contribution to the overall binding was weak.
Protein: DP04241 (UniProt P15146-3)
Region: residues 65	to 69
Annotation: phosphorylation display site (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We first confirmed a residue-specific phosphorylation of MAP2c on Tyr67 by tyrosine kinase Fyn (Fig. S4 in Supporting Information).
Protein: DP04241 (UniProt P15146-3)
Region: residues 288	to 294
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Presence of Grb2 reduced peak heights of unphosphorylated MAP2c in several regions (black circles in Fig. 6A). The most notable peak broadening was observed for the class I canonical SH3-binding site 288RTPPKSP294. The peak height decreased also in the proline-rich regions (residues 230–300) with multiple minimal SH3-binding PXXP motifs. Even stronger peak broadening was observed in a region between residues 185 and 198, rich in prolines, but lacking the PXXP motif. 
In addition to the class I SH3-binding motif 288RTPPKSP294, Grb2 interacts with residues 185 to 198 in the variable central region of MAP2c (cf. Fig. 6).
Protein: DP04241 (UniProt P15146-3)
Region: residues 185	to 198
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Presence of Grb2 reduced peak heights of unphosphorylated MAP2c in several regions (black circles in Fig. 6A). The most notable peak broadening was observed for the class I canonical SH3-binding site 288RTPPKSP294. The peak height decreased also in the proline-rich regions (residues 230–300) with multiple minimal SH3-binding PXXP motifs. Even stronger peak broadening was observed in a region between residues 185 and 198, rich in prolines, but lacking the PXXP motif. 
In addition to the class I SH3-binding motif 288RTPPKSP294, Grb2 interacts with residues 185 to 198 in the variable central region of MAP2c (cf. Fig. 6).
Protein: DP04241 (UniProt P15146-3)
Region: residues 60	to 70
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additional peak broadening of Fyn-phosphorylated MAP2c (compared to unphosphorylated MAP2c) in the presence of Grb2 revealed a phosphorylation-dependent binding site around pTyr67. The peak height was reduced below 50% for residues 60 to 70 (forest green circles in Fig. 6A).
Protein: DP04241 (UniProt P15146-3)
Region: residues 60	to 70
Annotation: SH2 domain binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additional peak broadening of Fyn-phosphorylated MAP2c (compared to unphosphorylated MAP2c) in the presence of Grb2 revealed a phosphorylation-dependent binding site around pTyr67. The peak height was reduced below 50% for residues 60 to 70 (forest green circles in Fig. 6A).
Broadening of the peak of pTyr67 below the detection limit showed that pTyr67 became a part of a large, well-ordered complex in the presence of Grb2. The same experiment was performed with Fyn-phosphorylated MAP2c and Grb2-SH2. Peak broadening was observed in the same region of the MAP2c sequence as with full-length Grb2 (pale green circles in Fig. 6A), confirming that pTyr67 interacts with the SH2 domain.
Protein: DP04241 (UniProt P15146-3)
Region: residues 60	to 70
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Additional peak broadening of Fyn-phosphorylated MAP2c (compared to unphosphorylated MAP2c) in the presence of Grb2 revealed a phosphorylation-dependent binding site around pTyr67. The peak height was reduced below 50% for residues 60 to 70 (forest green circles in Fig. 6A).
Broadening of the peak of pTyr67 below the detection limit showed that pTyr67 became a part of a large, well-ordered complex in the presence of Grb2. The same experiment was performed with Fyn-phosphorylated MAP2c and Grb2-SH2. Peak broadening was observed in the same region of the MAP2c sequence as with full-length Grb2 (pale green circles in Fig. 6A), confirming that pTyr67 interacts with the SH2 domain.
Protein: DP04242 (UniProt P45973)
Region: residues 1	to 21
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Secondary structure propensities predicted by TALOS N+ are in agreement with the high‐resolution structures of the individual CD and CSD, and suggested the presence of predominantly random coil conformation in the NTE, the HR, and the CTE (Figure 1c).
(a) Schematic of Hp1 dimer containing the ordered CD and CSD and disordered NTE, HR, and CTE.
In Figure 1 authors define NTE as the 1-21 region, HR as the hinge region 79-123, and CTE as 178-191 C-terminal region.
Protein: DP04242 (UniProt P45973)
Region: residues 79	to 123
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Secondary structure propensities predicted by TALOS N+ are in agreement with the high‐resolution structures of the individual CD and CSD, and suggested the presence of predominantly random coil conformation in the NTE, the HR, and the CTE (Figure 1c).
(a) Schematic of Hp1 dimer containing the ordered CD and CSD and disordered NTE, HR, and CTE.
In Figure 1 authors define NTE as the 1-21 region, HR as the hinge region 79-123, and CTE as 178-191 C-terminal region.
Protein: DP04242 (UniProt P45973)
Region: residues 178	to 191
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Secondary structure propensities predicted by TALOS N+ are in agreement with the high‐resolution structures of the individual CD and CSD, and suggested the presence of predominantly random coil conformation in the NTE, the HR, and the CTE (Figure 1c).
(a) Schematic of Hp1 dimer containing the ordered CD and CSD and disordered NTE, HR, and CTE.
In Figure 1 authors define NTE as the 1-21 region, HR as the hinge region 79-123, and CTE as 178-191 C-terminal region.
Protein: DP04242 (UniProt P45973)
Region: residues 178	to 191
Annotation: flexible C-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Secondary structure propensities predicted by TALOS N+ are in agreement with the high‐resolution structures of the individual CD and CSD, and suggested the presence of predominantly random coil conformation in the NTE, the HR, and the CTE (Figure 1c).
(a) Schematic of Hp1 dimer containing the ordered CD and CSD and disordered NTE, HR, and CTE.
In Figure 1 authors define NTE as the 1-21 region, HR as the hinge region 79-123, and CTE as 178-191 C-terminal region.
Protein: DP04242 (UniProt P45973)
Region: residues 79	to 123
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Secondary structure propensities predicted by TALOS N+ are in agreement with the high‐resolution structures of the individual CD and CSD, and suggested the presence of predominantly random coil conformation in the NTE, the HR, and the CTE (Figure 1c).
(a) Schematic of Hp1 dimer containing the ordered CD and CSD and disordered NTE, HR, and CTE.
In Figure 1 authors define NTE as the 1-21 region, HR as the hinge region 79-123, and CTE as 178-191 C-terminal region.
Protein: DP04242 (UniProt P45973)
Region: residues 1	to 21
Annotation: flexible N-terminal tail (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Secondary structure propensities predicted by TALOS N+ are in agreement with the high‐resolution structures of the individual CD and CSD, and suggested the presence of predominantly random coil conformation in the NTE, the HR, and the CTE (Figure 1c).
(a) Schematic of Hp1 dimer containing the ordered CD and CSD and disordered NTE, HR, and CTE.
In Figure 1 authors define NTE as the 1-21 region, HR as the hinge region 79-123, and CTE as 178-191 C-terminal region.
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 1	to 60
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
As the CD spectrum demonstrated that the structure of Prx was unfolded at physiological buffer conditions, we then used NMR to gain further insight into the solution‐state fold of Prx. 
The Streptococcus phage protein paratox is an intrinsically disordered protein
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 1	to 60
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
It can be clearly seen that in the absence of high‐salt or crowding agents, the 1H‐15N HSQC dispersion pattern of Prx at pH 7 is similar to that measured under denaturing conditions. Specifically, all backbone chemical shifts show low dispersion and are clustered between 8.0 and 8.6 ppm in the hydrogen dimension. This 1H‐15N HSQC pattern is diagnostic of a protein that lacks secondary structure and is disordered (Pandey et al., 2023; Prehna et al., 2014).
The Streptococcus phage protein paratox is an intrinsically disordered protein
Protein: DP04243 (UniProt A0A0H2UWN8)
Region: residues 1	to 60
Annotation: order (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
In contrast, the addition of unlabeled ComR DNA‐binding domain (DBD) to 15N‐labeled Prx results in a well resolved 1H‐15N HSQC indicative of an ordered and globular protein fold (Figure 3c).