LiteFold/DisProt huggingface dataset:
Protein: DP01281 (UniProt Q9JM54)
Region: residues 73	to 93
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Mcl-1 binds both NoxaA and NoxaB
Cross-references: PDB:2NL9
Protein: DP01282 (UniProt Q16576)
Region: residues 90	to 110
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure is well defined, except for the N terminus (residues 2–8), a segment comprising residues 90–109, and the C terminus (residues 409–425), for which the electron density is unclear due to structural disorder
Protein: DP01282 (UniProt Q16576)
Region: residues 409	to 425
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure is well defined, except for the N terminus (residues 2–8), a segment comprising residues 90–109, and the C terminus (residues 409–425), for which the electron density is unclear due to structural disorder
Protein: DP01283 (UniProt Q9Y3E7)
Region: residues 184	to 199
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
residues 184–199 do not contribute to the interaction and are disordered in the structure.
Protein: DP01283 (UniProt Q9Y3E7)
Region: residues 184	to 199
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here we present structural evidence for a closed and open conformation of full length CHMP3, which confirms the activated state represented by the CHMP3 crystal structure. Both conformations do not reveal any changes in their secondary structure content or in their overall thermal stability, indicating that a first step in activation entails detachment of the C-terminal module from the N-terminal core.
Protein: DP01284 (UniProt P24928)
Region: residues 1773	to 1970
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Human RNA polymerase II CTD heptads 27-52 is predominantly disordered.
Protein: DP01284 (UniProt P24928)
Region: residues 1773	to 1970
Annotation: microfibril binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Dark-state exchange saturation transfer (DEST) NMR probes the binding of CTD27-52 WT to sonicated TAF15 fibrils
However, in the presence of sonicated fibrils we reliably observe decreased peak intensity and increased transverse relaxation, ΔR2, of CTD27-52 which can be explained by transient binding of CTD27-52 to the high molecular weight fibrillar segments25.
Protein: DP01284 (UniProt P24928)
Region: residues 1773	to 1960
Annotation: microfibril binding (Molecular function)
Evidence: fluorescence microscopy evidence used in manual assertion
Supporting statements:
As previously observed5, high avidity binding of the CTD27-52 in solution corresponds to CTD27-52 fluorescence localization around the outer ring of each mCherry-TAF15 LC hydrogel.
However, when dilute CTD Δ1961-1970 is incubated with intact TAF15 hydrogels, CTD Δ1961-1970 fluorescence localization and recovery after photobleaching are almost identical to that of WT (the half life and diffusion rate of CTD Δ1961-1970 were 56.6 ± 7.1 seconds and 0.096 ± 0.012 μm2/s, respectively, compared to 58.0 ± 0.3 seconds and 0.094 ± 0.001 μm2/s for WT) (Figure S8D–E).
Protein: DP01285 (UniProt Q97W59)
Region: residues 18	to 139
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Figure 6 clearly shows that only the N-terminal α-helical parts of aIF2β (residues 5–17) retain their positions in all known structures. The conformations of the central parts and zinc-binding domains of aIF2β vary in each structure
Protein: DP01286 (UniProt Q7Z094)
Region: residues 36	to 46
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Indeed, apart from the first few residues, the structure is well defined up to around residue 35 and does adopt an ICK structure.
The C-terminal region, including Phe44, is disordered.
Thus, even though the regions of conformational space sampled by the families of structures of ι-RXIA and ι-RXIA[l-Phe44] differ slightly in Figure 6, no conclusions can be drawn about the solution conformations of the C-terminal tail containing Phe44 other than that they are disordered in both cases.
Protein: DP01287 (UniProt Q9VZU1)
Region: residues 241	to 388
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
A high level of disorder in dLBD is revealed by the limited amide proton chemical shift dispersion in 15N HSQC spectra.
Protein: DP01287 (UniProt Q9VZU1)
Region: residues 241	to 388
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We demonstrate that the long intrinsically disordered C-terminal domain of ASCIZ binds LC8 to form a dynamic ensemble of complexes.
Protein: DP01287 (UniProt Q9VZU1)
Region: residues 241	to 388
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The dLBD CD spectrum has a large negative ellipticity at 200 nm, indicating that it is primarily disordered.
Protein: DP01288 (UniProt O43313)
Region: residues 362	to 823
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
We similarly assessed the gel mobility of complexes formed by LC8 and the LC8-binding domain of human ASCIZ (hLBD).
Molecular sieving is the dominate effect on hLBD mobility as both hLBD and dLBD are disordered and highly extended.
hLBD:LC8 complexes form a dynamic ensemble....Titration of the hLBD with LC8 by size-exclusion chromatography (Fig 4d) supports our interpretation of the native gel experiments in Fig 4c.
Protein: DP01289 (UniProt Q9KMA5)
Region: residues 1	to 36
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Together with the CD data, this thus agrees with a model in which the VcHigA2 antitoxin has a well-structured dimeric C-terminal domain, as seen in the crystal structure, and ~36 amino acids long disordered N-terminal segment.
Protein: DP01289 (UniProt Q9KMA5)
Region: residues 1	to 36
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of the N-terminal region in its native state (attached to the C-terminal domain) was estimated by calculating the difference spectrum between full length VcHigA2 and a truncate (VcHigA2ΔN) consisting of amino acid residues 37–104. The latter protein, which mirrors the residues seen in the crystal structure, is thermodynamically stable and shows a CD spectrum with essentially the same α-helical content as the full length protein (Figure ​(Figure2B). The difference spectrum is similar to the spectrum of the isolated peptide and suggests presence of the random coil structure (gray and blue curves, Figure2B).
Protein: DP01289 (UniProt Q9KMA5)
Region: residues 1	to 36
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The interaction between VcHigA2 and VcHigB2 is characterised by a very high affinity and by structuring of the antitoxin N-terminal domain. Coupled folding and binding is evident from the comparison of the CD spectra from free and the VcHigB2-bound VcHigA2.
Protein: DP01289 (UniProt Q9KMA5)
Region: residues 1	to 36
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Several lines of evidence suggest that the VcHigA2 N-terminal region (residues 1–36), which was not observed in the crystal structure of the free antitoxin, is intrinsically disordered in solution.
Cross-references: PDB:5J9I
Protein: DP01289 (UniProt Q9KMA5)
Region: residues 3	to 33
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum of a peptide encompassing residues Asn3 to Asn33 is typical for a random coil polypeptide with a minimum below 200 nm and a very weak ellipticity above 210 nm.
Protein: DP01289 (UniProt Q9KMA5)
Region: residues 3	to 22
Annotation: toxin sequestering activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The minimal element for toxin inhibition is the VcHigA2 peptide encompassing residues Asn3-Glu22, which corresponds to the segment that folds into an α-helix upon toxin binding (see below). Using an in vitro ribosome binding assay we also observe that the VcHigA23-22 peptide prevents VcHigB2 binding to the ribosomes (Figure ​(Figure3B).3B). Thus the intrinsically disordered N-terminal domain is sufficient for VcHigB2 toxin regulation.
Cross-references: PDB:5JAA
Protein: DP01289 (UniProt Q9KMA5)
Region: residues 1	to 36
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The dissociation constant of the VcHigB2–VcHigA2 complex is 50 pM.
The negative enthalpy change likely originates from the folding of the N-terminal domain (in particular the formation of an α-helix) and from specific interactions between VcHigB2 and VcHigA2.
Protein: DP01289 (UniProt Q9KMA5)
Region: residues 3	to 36
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The N-terminal region of VcHigA2 folds into an N-terminal α-helix (residues 3–22) followed by a short β-strand (residues 28–37).
Cross-references: PDB:5JAA
Protein: DP01289 (UniProt Q9KMA5)
Region: residues 3	to 36
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The minimal element for toxin inhibition is the VcHigA2 peptide encompassing residues Asn3-Glu22, which corresponds to the segment that folds into an alpha-helix upon toxin binding.
Cross-references: PDB:5JAA
Protein: DP01291 (UniProt P0AE72)
Region: residues 48	to 82
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
MazE  is  an  82-amino  acid  protein  (98amino acids in the used His-tagged construct), but in our crystal structure only 44 residues located in the N-terminal half of the sequence are found ordered. SDS-gel analysis of redissolved crystals nevertheless indicated that in the crystal the protein is intact. Lack of structure of the C-terminal half is thus not a consequence  of  proteolytic  degradation  of  the  sample.  This makes  MazE  a  member  of  the  growing  class  of  intrinsicallyunstructured  proteins  that  become  structured  upon  binding their natural partners. 
Cross-references: PDB:1MVF
Protein: DP01291 (UniProt P0AE72)
Region: residues 51	to 82
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Information about the dynamical behavior of both full-length and truncated EcMazEs in their free form was obtained by measuring {1H}-15N steady state NOEs (Supplementary Figure S2). Small and negative {1H}-15N NOEs are indicative of higher flexibility and they are observed mainly for the N-terminal residues (His-tag) and in the disordered C-terminal domain, in agreement with the lack of density in the crystal for the C-terminal tails of full-length EcMazE. Moreover, lack of chemical shift dispersion and high intensity peaks of the C-terminal domain in full-length EcMazE (Figure ​(Figure1B,1B, inset) confirms the high flexibility of this region.
Multiple complementary techniques including
NMR, SAXS and ITC show that the long intrinsically
disordered C-termini in MazE, required for MazF neutralization, does not affect the interactions between
the antitoxin and its operator. Rather, the MazE Cterminus plays an important role in the MazF binding,
which was found to increase the MazE affinity for the
palindromic single site operator
Structures 2MRU and 2MRN are of the MazE 1-50 structured region in isolation and bound to DNA, and were used to derive the disordered state of the C terminal tail in the NMR and SAXS experiments
Cross-references: BMRB:25093
PDB:2MRU
PDB:2MRN
Protein: DP01291 (UniProt P0AE72)
Region: residues 51	to 82
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
The major source of variability required for a good agreement with the SAXS data is likely attributed to the flexible C-terminus.
None of the two normalized Kratky return to zero, indicating the presence of highly flexible regions in the scattering particle mainly due to the His-tag in both complexes and increased flexibility is even more present in the full-length EcMazE–DNA ‘a’ complex due to the extended disordered C-terminal tails, missing in the EcMazE1–50–DNA ‘a’ complex.
We determined an accurate structural model of the EcMazE–DNA complex using a combination of NMR and SAXS. This structure is in agreement with previous mutagenesis data and confirms that the C-terminal tail of EcMazE remains disordered and is not directly involved in DNA-binding upon interaction between the N-terminal EcMazE domain with DNA.
Complementary to validating our NMR EcMazE1–50-DNA structure, we aimed to investigate the structural dynamics of the DNA-binding domain and the extended toxin-neutralizing domain in the full-length protein (...) Furthermore, a comparison between the normalized Kratky plots of both EcMazE–DNA complexes (Figure
7D) reveals that the EcMazE1–50-DNA shows diminished internal flexibility compared to full-length EcMazE-DNA. This is in perfect agreement with our NMR relaxation data (Supplementary Figure S2), and can be explained by the absence of the long disordered C-terminal tail in the truncated EcMazE1–50.(....) None of the two normalized Kratky return to zero, indicating the presence of highly flexible regions in the scattering particle mainly due to the His-tag in both complexes and increased flexibility is even more present in the full-length EcMazE–DNA ‘a’ complex due to the extended disordered C-terminal tails, missing in the EcMazE1–50– DNA ‘a’ complex
Protein: DP01291 (UniProt P0AE72)
Region: residues 48	to 76
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The C-terminal region, unstructured in the free form of MazE, becomes structured in complex with toxin MazF.
Interactions between MazE and MazF are primarily mediated by the C 
terminus of MazE, which wraps around the MazF homodimer crossing the edge of the MazF dimer interface and draping primarily over the medial MazF protomer (Figure 2).
Cross-references: PDB:1UB4
Protein: DP01291 (UniProt P0AE72)
Region: residues 48	to 76
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
MazE (antidote) and MazF (toxin) form a linear heterohexamer composed of alternating toxin and antidote homodimers (MazF(2)-MazE(2)-MazF(2)). The MazE homodimer contains a beta barrel from which two extended C termini project, making interactions with flanking MazF homodimers that resemble the plasmid-encoded toxins CcdB and Kid. The MazE/MazF heterohexamer structure documents that the mechanism of antidote-toxin recognition is common to both chromosomal and plasmid-borne addiction modules, and provides general molecular insights into toxin function, antidote degradation in the absence of toxin, and promoter DNA binding by antidote/toxin complexes.
Numerous van der Waals, polar, and salt-bridge interactions among conserved residues stabilize the conformation of residues 68–76 of MazE as it meanders across the basic underside of the MazF homodimer (Figure 5A).
Site 2 is almost exclusively hydrophobic in nature and represents the most extensive contact interface between MazE and MazF (buried solvent accessible surface area = 1170 Å2, Figure 5B). Residues 54–67 of MazE and three segments of the MazF polypeptide chain support interactions within site 2, including the S3-S4 loop, α helix H1# (# denotes the lateral MazF protomer), and the C terminus of α helix H3 (Figure 1B).
Site 3 interactions between MazE and MazF bury approximately 410 Å2 of solvent-accessible surface areas, and involve residues 48–53 of MazE plus the medial monomer of MazF. Within the site 3 segment of MazE (residues 51–54), Pro 51 and a conserved aromatic residue (Phe53) make van der Waals interactions with α helix H3 (residues Gln100, Leu101, and Ala104) of the medial MazF protomer as the polypeptide chain of the antidote meanders across the hydrophobic surface of the toxin homodimer Figure 4, Figure 5.
Cross-references: PDB:1UB4
Protein: DP01291 (UniProt P0AE72)
Region: residues 51	to 82
Annotation: DNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
However, addition of a variable amount of EcMazF to a lower concentration of EcMazE (1 μM), which is not sufficient to cause a shift of the DNA band by itself, results in an increase in affinity for EcMazE to DNA (Figure ​3B). At very high EcMazF:EcMazE ratios, this effect is abolished and coincides with a reduced shift of the band corresponding to the complex. Thus, EcMazF enhances the binding of EcMazE to their DNA operator fragment ‘a’ though its interaction with the C-terminal region of EcMazE.
Superposition of our EcMazE–DNA complex on the crystal structure of the EcMazE–EcMazF complex (32) (Supplementary Figure S8C) indicates additional protein–DNA interaction via the flanking basic regions of the EcMazF homodimer. This favors a model where the enhancement in DNA binding by EcMazF is caused by co-operative binding of the antitoxin and toxin to the DNA instead of an allosteric effect.
Protein: DP01291 (UniProt P0AE72)
Region: residues 68	to 82
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Central in this regulation is an EcMazE-induced double conformational change as follows: a rearrangement of a crucial active site loop and a relative rotation of the two monomers in the EcMazF dimer. Both are induced by the C-terminal residues Asp-78–Trp-82 of EcMazE, which are also responsible for strong negative cooperativity in EcMazE-EcMazF binding
To investigate the interaction between EcMazF and residues Asp-78–Trp-82 of EcMazE, we determined the crystal structure of EcMazFE24A in complex with EcMazE(68– 82). In our structures, Pro-76–Trp-82 forms a -hairpin, the presence of which prevents loop 1-2 of both EcMazF monomers to adopt the catalytically competent conformation and simultaneously blocks both substrate-binding sites on the EcMazF dimer

Cross-references: PDB:5CQY
PDB:5CQX
Protein: DP01291 (UniProt P0AE72)
Region: residues 68	to 82
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Central in this regulation is an EcMazE-induced double conformational change as follows: a rearrangement of a crucial active site loop and a relative rotation of the two monomers in the EcMazF dimer. Both are induced by the C-terminal residues Asp-78–Trp-82 of EcMazE, which are also responsible for strong negative cooperativity in EcMazE-EcMazF binding
To investigate the interaction between EcMazF and residues Asp-78–Trp-82 of EcMazE, we determined the crystal structure of EcMazFE24A in complex with EcMazE(68– 82). In our structures, Pro-76–Trp-82 forms a -hairpin, the presence of which prevents loop 1-2 of both EcMazF monomers to adopt the catalytically competent conformation and simultaneously blocks both substrate-binding sites on the EcMazF dimer

Cross-references: PDB:5CQY
PDB:5CQX
Protein: DP01291 (UniProt P0AE72)
Region: residues 68	to 82
Annotation: toxin sequestering activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Central in this regulation is an EcMazE-induced double conformational change as follows: a rearrangement of a crucial active site loop and a relative rotation of the two monomers in the EcMazF dimer. Both are induced by the C-terminal residues Asp-78–Trp-82 of EcMazE, which are also responsible for strong negative cooperativity in EcMazE-EcMazF binding
To investigate the interaction between EcMazF and residues Asp-78–Trp-82 of EcMazE, we determined the crystal structure of EcMazFE24A in complex with EcMazE(68– 82). In our structures, Pro-76–Trp-82 forms a -hairpin, the presence of which prevents loop 1-2 of both EcMazF monomers to adopt the catalytically competent conformation and simultaneously blocks both substrate-binding sites on the EcMazF dimer

Cross-references: PDB:5CQY
PDB:5CQX
Protein: DP01291 (UniProt P0AE72)
Region: residues 50	to 82
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Central in this regulation is an EcMazE-induced double conformational change as follows: a rearrangement of a crucial active site loop and a relative rotation of the two monomers in the EcMazF dimer. Both are induced by the C-terminal residues Asp-78–Trp-82 of EcMazE, which are also responsible for strong negative cooperativity in EcMazE-EcMazF binding
E24A Mutation Does Not Affect Antitoxin Recognition—We next compared the binding of the intrinsically disordered domain of EcMazE (EcMazE(50– 82)) to EcMazF and EcMazFE24A using ITC (Table 2 and Fig. 6). We find that both EcMazF and EcMazFE24A possess two binding sites for EcMazE(50– 82). Binding is sequential and with strong negative cooperativity. The first EcMazE(50– 82) molecule binds with an affinity around 10 nM, although subsequent binding of the second EcMazE(50– 82) is 3 orders of magnitude weaker. This cooperativity is largely due to the C-terminal EcMazE residues Asp-78–Trp-82 (Table 2 and Fig. 6).
Protein: DP01292 (UniProt P49768)
Region: residues 1	to 77
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 77 residues have no EM density and are presumably disordered, likely due to their intrinsic flexibility.
Cross-references: EMDB:3061
PDB:5A63
Protein: DP01292 (UniProt P49768)
Region: residues 262	to 378
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The extended sequences between TM6 and TM7 harbor the site of autocatalytic cleavage; but these sequences are hydrophilic and mostly disordered (Fig. 2b).
Cross-references: PDB:5A63
EMDB:3061