LiteFold/DisProt huggingface dataset:
Protein: DP02531 (UniProt S6B291)
Region: residues 240	to 465
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The CH1 domain is intrinsically unfolded in the absence of CL and binds to the molecular chaperone BiP. Only when the heavy chain engages the light chain can CH1 be released from BiP to allow a fully assembled IgG molecule to be secreted
Cross-references: PDB:4LLY
PDB:4LLW
Protein: DP02532 (UniProt Q07866)
Region: residues 185	to 208
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
It should be noted that the 24 N-terminal residues (185–208) from KLC1-TPR[A1-B5], as well as the 21-residue stretch containing the His-tag and the thrombine cleavage site, were not modeled due to electron density absence.
Cross-references: PDB:5OJ8
Protein: DP02533 (UniProt P56696)
Region: residues 550	to 593
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 524-549 of Kv7.4 and all of CaM except for a few residues at the N-terminus and in the loop interdomain linker (residues 78-82) were resolved. 
Cross-references: PDB:4GOW
Protein: DP02534 (UniProt O70201)
Region: residues 123	to 140
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This helix terminates at residue Lys-120 with residue Asn-122, the last observed in the electron density. The last eighteen residues are not observed in the crystal structure, but these can be accommodated in the solvent continuum.
Cross-references: PDB:1M4M
Protein: DP02535 (UniProt Q8R4T5)
Region: residues 120	to 130
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The blue and magenta dotted lines represent the disordered β2–β3 loops
Cross-references: PDB:2EGN
PDB:2EGK
PDB:2EGO
Protein: DP02535 (UniProt Q8R4T5)
Region: residues 1	to 96
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
However, crystallization of the N-terminal region, Tamalin1–189, was unsuccessful. Thus, we performed limited proteolysis to analyze its domain architecture, and expressed the PDZ domain for biochemical characterization.
Protein: DP02535 (UniProt Q8R4T5)
Region: residues 1	to 96
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
To detect intrinsic ligand binding, we expressed high levels of the Tamalin mutant, which lacks the unstructured AR region as shown by circular dichroism spectra (Supplementary Figure 1), and its derivatives.
The difference spectrum (grey)
between Tamalin1-189 (red) and the PDZ domain (blue) is derived from the unstructured AR region.
Protein: DP02536 (UniProt P15825)
Region: residues 74	to 348
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the model of the H.marismortui 50S reported by Ban et al. (2000), L10 was not included because of difficulty in map interpretation in this region. As refinement progressed, map quality improved and small segments of L10 were identified and modeled. Two α‐helices corresponding to residues 12–29 and 63–73 have been included in this model.
Cross-references: PDB:1JJ2
Protein: DP02536 (UniProt P15825)
Region: residues 30	to 62
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the model of the H.marismortui 50S reported by Ban et al. (2000), L10 was not included because of difficulty in map interpretation in this region. As refinement progressed, map quality improved and small segments of L10 were identified and modeled. Two α‐helices corresponding to residues 12–29 and 63–73 have been included in this model.
Cross-references: PDB:1JJ2
Protein: DP02537 (UniProt P30130)
Region: residues 46	to 69
Annotation: protein binding (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
In this structure, FimF has already polymerized with FimG, and the N-terminal domain of FimD swings over to bind CTD2; the N-terminal domain maintains contact with FimC-FimF, while at the same time permitting access to the C-terminal domains.
Cross-references: PDB:6E15
Protein: DP02537 (UniProt P30130)
Region: residues 1	to 46
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In this conformation, the FimD N-tail is not visible, likely due to flexibility, which is in agreement with previous structures of the disengaged NTD 13,14,20.
Cross-references: PDB:6E14
EMDB:8953
Protein: DP02537 (UniProt P30130)
Region: residues 499	to 518
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence in the PDB shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:6E14
EMDB:8953
Protein: DP02538 (UniProt Q16790)
Region: residues 38	to 136
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
in size exclusion chromatography (SEC), PG(38–136) eluted with an anomalous retention
volume (10.68 ml), corresponding to an apparent molecular
mass of 50 kDa much greater than the expected one
Protein: DP02538 (UniProt Q16790)
Region: residues 38	to 136
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
the high number of acidic Glu and Asp residues in the primary sequence caused a scarce denaturation of the protein in SDS [25, 62], which resulted in an aberrant migration on SDS-PAGE, leading to an apparent molecular mass between 15 and 20 kDa instead of the expected 10.8 kDa
Protein: DP02538 (UniProt Q16790)
Region: residues 38	to 136
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
By DLS analysis, a monodisperse peak (17% of
polydispersity) was evident, indicative of a species homogeneous in size distribution with a rather large apparent hydrodynamic radius (4.1 nm ± 0.7).
Protein: DP02538 (UniProt Q16790)
Region: residues 38	to 136
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In agreement with the hypothesis that PG(38–136) is an IDP, collected spectrum showed a strong negative molar ellipticity value at 198 nm and a negative band between 210 and 230 nm (Fig.  3a), indicative of a protein in a largely disordered conformation.
In conclusion, collected far-UV-CD data give strong evidence that PG (38–136) is an IDP possessing some residues in PPII conformation.
Protein: DP02538 (UniProt Q16790)
Region: residues 38	to 136
Annotation: molecular function activator activity (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
In the same paper, our finding proved that the PG domain was able to assist the catalysis mediated by the CA domain. 
CA domain was titrated with diferent concentrations of PG (38–136) and the catalytic activity was evaluated. In agreement with the previous results, it was observed that 10 µM PG(38–136) was able to increase the CA catalytic activity of about 63%.
Protein: DP02538 (UniProt Q16790)
Region: residues 38	to 136
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1D [1H] NMR spectrum (Fig. S3a) together with the 2D [1H, 1H] TOCSY (Total Correlation Spectroscopy) [32] and 2D [1H, 1H] NOESY (Nuclear Overhauser
Enhancement Spectroscopy) [33] experiments (Fig. S3b) appear typical of IDPs. In particular, the 1D [1H] (Fig. S3a) and 2D [1H, 1H] TOCSY (Fig. S3b left panel) spectra present low chemical shift dispersion with the backbone amide HN protons resonating in the narrow random coil range between 8 and 8.6 ppm.
Protein: DP02538 (UniProt Q16790)
Region: residues 38	to 136
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The incubation of PG(38–136) with trypsin protease at diferent ratios showed a complete cleavage in the early hours of the reaction.
Protein: DP02539 (UniProt Q16611)
Region: residues 64	to 98
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism (CD) spectra reveal that the BH3 peptides investigated are mainly
disordered under our experimental conditions. However, the percentage helicities of the
BH3 peptides calculated from MRE value at 222 nm19, ranges between approximately 9-
63%.
These BCL-2 family proteins have a homologous BH3 domain, which is intrinsically disordered in isolation, but form a contiguous helical segment upon binding to its partner BCL-2 proteins
Protein: DP02539 (UniProt Q16611)
Region: residues 75	to 84
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
the Bak peptide adopts an amphipathic alpha helix that interacts with Bcl-xL through hydrophobic and electrostatic interactions
Cross-references: PDB:1BXL
Protein: DP02539 (UniProt Q16611)
Region: residues 64	to 98
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
As expected, the effector, pro-apoptotic peptides BAK and BAX bind less tightly
than the activator proteins.
We show that eight different disordered BH3 proteins all bind to their BCL-2 partner (MCL-1) very rapidly, and that the differences in sequences result in different dissociation rates.
Protein: DP02539 (UniProt Q16611)
Region: residues 64	to 98
Annotation: molecular function regulator (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
As expected, the effector, pro-apoptotic peptides BAK and BAX bind less tightly
than the activator proteins.
We show that eight different disordered BH3 proteins all bind to their BCL-2 partner (MCL-1) very rapidly, and that the differences in sequences result in different dissociation rates.
Protein: DP02539 (UniProt Q16611)
Region: residues 69	to 86
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The BAK segment forms an alpha-helix on the surface of Bcl-xL.
Cross-references: PDB:5FMK
Protein: DP02539 (UniProt Q16611)
Region: residues 69	to 86
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The BAK segment forms an alpha-helix on the surface of Bcl-xL.
Cross-references: PDB:5FMK
Protein: DP02540 (UniProt Q07812)
Region: residues 49	to 83
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism (CD) spectra reveal that the BH3 peptides investigated are mainly
disordered under our experimental conditions. However, the percentage helicities of the
BH3 peptides calculated from MRE value at 222 nm19, ranges between approximately 9-
63%
These BCL-2 family proteins have a homologous BH3 domain, which is intrinsically disordered in isolation, but form a contiguous helical segment upon binding to its partner BCL-2 proteins
Protein: DP02540 (UniProt Q07812)
Region: residues 49	to 83
Annotation: protein binding (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
As expected, the effector, pro-apoptotic peptides BAK and BAX bind less tightly
than the activator proteins.
Protein: DP02540 (UniProt Q07812)
Region: residues 49	to 83
Annotation: molecular function regulator (Molecular function)
Evidence: fluorescence evidence used in manual assertion
Supporting statements:
As expected, the effector, pro-apoptotic peptides BAK and BAX bind less tightly
than the activator proteins.
Protein: DP02540 (UniProt Q07812)
Region: residues 55	to 79
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Here, we describe crystal structures of the pro-survival proteins Mcl-1 and Bcl-x(L) in complex with a 34-mer peptide from Bax that encompasses its BH3 domain. These structures reveal canonical interactions between four signature hydrophobic amino acids from the BaxBH3 domain and the BH3-binding groove of the pro-survival proteins.
The boundaries of the helical segment were derived from the PDB file.
Cross-references: PDB:3PK1
Protein: DP02541 (UniProt P0ACN7)
Region: residues 1	to 67
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We used nuclear magnetic resonance (NMR) spectroscopy to characterize the CytR DBD free in solution and to determine the high-resolution structure of a CytR DBD monomer bound specifically to one DNA half-site of the uridine phosphorylase (udp) operator. We find that the free DBD populates multiple distinct conformations distinguished by up to four sets of NMR peaks per residue.
We began our studies of the DBD free state and first assessed the structure and stability of the protein by collecting 15N HSQC NMR spectra over a range of temperatures. As the temperature is increased, the dispersion of the peaks is reduced, indicating that the protein unfolds until only one set of random coil-like signals is obtained at 35 °C
Cross-references: PDB:2LCV
Protein: DP02541 (UniProt P0ACN7)
Region: residues 9	to 55
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
These stable structures coalesce into a single, more stable udp-bound form that features a three-helix bundle containing a canonical helix-turn-helix motif.
In the presence of the udp half-site DNA, we find a single set of well-dispersed DBD peaks in the NMR spectrum. This peak pattern exists at 20 °C and remains above 35 °C (Figure 1B). The structural consequences of DNA binding are reversible for DNA substrates; removal of DNA results in the return of the original DBD HSQC spectrum that reflects multiple protein conformations.
Cross-references: PDB:2LCV
Protein: DP02541 (UniProt P0ACN7)
Region: residues 1	to 67
Annotation: DNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the presence of the udp half-site DNA, we find a single set of well-dispersed DBD peaks in the NMR spectrum. This peak pattern exists at 20 °C and remains above 35 °C (Figure 1B). The structural consequences of DNA binding are reversible for DNA substrates; removal of DNA results in the return of the original DBD HSQC spectrum that reflects multiple protein conformations.
When associated with DNA, the DBD is a three-helix bundle containing a canonical helix–turn–helix motif.
Cross-references: PDB:2LCV
Protein: DP02541 (UniProt P0ACN7)
Region: residues 1	to 67
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The structure and stability of the free-state DBD were probed further using CD spectroscopy. The far-UV CD spectrum (Figure 2A) indicates primarily α-helix and random coil. The secondary structure composition was estimated using CDSSTR as implemented in CDPro.(22) The reconstructed spectrum that gave the best fit (Figure 2A) predicts a helical content of 22% at 20 °C, with the remainder predicted to be random coil.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 1	to 67
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
In the case of the free-state DBD, no peaks were detectable in the NMR 15N HSQC spectrum within 10 min of the transfer into D2O, revealing complete amide proton exchange.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 9	to 55
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy-based hydrogen-deuterium exchange evidence used in manual assertion
Supporting statements:
In the case of the free-state DBD, no peaks were detectable in the NMR 15N HSQC spectrum within 10 min of the transfer into D2O, revealing complete amide proton exchange. In contrast, with the DBD bound to the udp half-site, we find that 30 peaks are present in the NMR spectrum following resuspension in D2O (Figure 1C). These amide protons of the DBD–DNA complex exchange more slowly than those exposed to solvent, suggesting that they are involved in stable secondary structure or are buried within the protein interior or the protein–DNA interface.
The exchange-protected residues of the DNA-bound form reside in this segment of the protein.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 9	to 55
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The reconstructed spectrum that gave the best fit (Figure 2A) predicts a helical content of 22% at 20 °C, with the remainder predicted to be random coil. This is equivalent to only 15 residues in a helical conformation, slightly more than half the number of helical residues that we find in the bound form.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 1	to 67
Annotation: DNA binding (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
We used the fluorescence anisotropy of a dye-conjugated (Alexa 532) DNA substrate to monitor the binding of the CytR DBD to DNA. Results of titration experiments (Figure 3) indicate that the CytR DBD binds the udp operator left half-site. We analyzed titration data assuming a 1:1 stoichiometry between monomeric protein and DNA.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 1	to 67
Annotation: molecular function regulator (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
We used the fluorescence anisotropy of a dye-conjugated (Alexa 532) DNA substrate to monitor the binding of the CytR DBD to DNA. Results of titration experiments (Figure 3) indicate that the CytR DBD binds the udp operator left half-site. We analyzed titration data assuming a 1:1 stoichiometry between monomeric protein and DNA.
The cytidine repressor (CytR) is a member of the LacR family of bacterial repressors with distinct functional features. The Escherichia coli CytR regulon comprises nine operons whose palindromic operators vary in both sequence and, most significantly, spacing between the recognition half-sites.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 1	to 66
Annotation: disorder (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The backbone amide resonances of CytRN are dispersed over a narrow chemical shift range between 7.9 and 8.8 ppm in the 1H dimension, and backbone (1HN, 15N, 13C′, 13Cα, 13Cβ, and 1Hα) chemical shifts correlate well with random coil values (fig. S2A), confirming that CytRN is intrinsically disordered. 
Most of the resonances visible in the HSQC spectrum of CytR (Fig. 1D, black contours) overlay very well with matching resonances from CytRN (Fig. 1D, orange contours), indicating that the N-terminal DBD is unstructured in full-length CytR also.
Protein: DP02541 (UniProt P0ACN7)
Region: residues 35	to 45
Annotation: pre-molten globule (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
Residue-specific secondary structure propensity (SSP) (32) scores, calculated using backbone chemical shifts, indicate that native CytRN does not adopt stable secondary structure, although it has up to ~30% residual helicity in regions of the protein that form helices in the DNA-bound conformation (Fig. 1C) (33). This conclusion is consistent with residue-specific patterns in 13Cα and 13C′ secondary chemical shifts that suggest the presence of a low degree of helical content between residues M12-K18 and K35-E45 within an overall disordered ensemble (fig. S2B).
Protein: DP02541 (UniProt P0ACN7)
Region: residues 11	to 56
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
In contrast, the rest of the protein from T11 to Q56 undergoes sizeable changes in chemical shift upon transitioning to the excited state with an average CSP of 0.59 ± 0.25 ppm over 44 residues, underscoring the fact that disordered native CytR acquires a globally folded structure in the excited state.The magnitude of CSPs plotted on the structure of DNA-bound CytRN (fig. S12) also illustrates that CSPs are not localized to a particular region but are instead distributed across the entire protein sequence from T11 to Q56.
Figure 2G shows the residue-specific S2 values of the excited state evaluated from 15N, 1HN, 13Cα, and 13C′ chemical shift information. S2 values are high in the interior of CytRN and range between 0.60 and 0.88, consistent with the rigidity expected from a globally folded excited state conformation. On the other hand, S2 values drop to less than 0.5 for the flexible terminal residues M1 to M12 and P57 to E66 (Fig. 2G). 
We then acquired CEST data on a sample containing 628 μM 15N-labeled CytRN and 150 μM uridine phosphorylase (udp) half-site double-stranded DNA, which is one of the operator regions specifically recognized by CytRN (33). In the presence of cognate DNA, a distinct third dip in intensity can be clearly discerned in the CEST profile of CytRN D34 at the 15N chemical shift of state B (117.2 ppm) which is the direct result of exchange between free and DNA-bound forms of CytRN (Fig. 4A).
Protein: DP02541 (UniProt P0ACN7)
Region: residues 1	to 66
Annotation: order (Structural state)
Evidence: nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
We then calculated the structure of the excited state of CytRN using CS-Rosetta (52, 53) incorporating 119 backbone chemical shifts and 65 15N-1H RDCs as structural restraints (Fig. 3C and Supplementary Text). A well-defined funnel is observed in the energy versus root mean square deviation (RMSD) plot, confirming that the structure calculations have converged (fig. S16).
CytRN adopts a three-helix bundle topology in the excited state, in which helix 3 (H3) docks on to the HTH motif formed by helices 1 (H1) and 2 (H2) (Fig. 3C).