LiteFold/DisProt huggingface dataset:
Protein: DP00288 (UniProt Q06253)
Region: residues 1	to 73
Annotation: protein binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Doc modulates the affinity of Phd for the operator region of the operon as observed in electrophoretic mobility shift assays (Figure 3B). At increasing Doc:Phd ratios between 0 and 1, the band corresponding to unbound DNA disappears and a series of distinct bands appear that we interpret in terms of Phd/Doc/DNA complexes of variable stoichiometry. A first Doc molecule will bridge the two Phd dimers bound to their two sites on the operator DNA and increase affinity through an avidity effect. This interaction will recruit both the high- and low-affinity sites on Doc. A second and third Doc molecule will bind through their high-affinity sites on the two free Phd C termini of the DNA-bound Phd2-Doc-Phd2 complex, resulting in a Doc-Phd2-Doc-Phd2-Doc operator DNA complex.
Protein: DP00288 (UniProt Q06253)
Region: residues 1	to 73
Annotation: DNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Doc modulates the affinity of Phd for the operator region of the operon as observed in electrophoretic mobility shift assays (Figure 3B). At increasing Doc:Phd ratios between 0 and 1, the band corresponding to unbound DNA disappears and a series of distinct bands appear that we interpret in terms of Phd/Doc/DNA complexes of variable stoichiometry. A first Doc molecule will bridge the two Phd dimers bound to their two sites on the operator DNA and increase affinity through an avidity effect. This interaction will recruit both the high- and low-affinity sites on Doc. A second and third Doc molecule will bind through their high-affinity sites on the two free Phd C termini of the DNA-bound Phd2-Doc-Phd2 complex, resulting in a Doc-Phd2-Doc-Phd2-Doc operator DNA complex.
Protein: DP00288 (UniProt Q06253)
Region: residues 1	to 73
Annotation: protein binding (Molecular function)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Our mechanistic model for conditional cooperativity predicts that at saturating levels of Doc, a Doc-Phd2-Doc heterotetrameric complex that is far less capable of repressing the phd/doc operon is formed. We used SAXS to characterize this complex and examine its shape and dimensions. Based on our crystal structure, we constructed a series of alternative Phd/Doc complexes with different stoichiometries (including Phd2-Doc-Phd2, Doc-Phd2-Doc, and the two possible Phd2-Doc architectures). The comparison of the experimental scattering data to the calculated scattering curves derived from these models reveals a close correspondence only to the Doc-Phd2-Doc model and very poor fits to other architectures (Table S1). The Rg (27.5 Å) calculated from the Guinier analysis and the bimodal shape and maximum dimension of the particle (Dmax = 85 Å) obtained from the distance distribution function (P(r)) all agree with our V-shaped model of the Doc-Phd2-Doc complex. Moreover the P(r) function and Kratky plot are consistent with a properly folded, homogeneous, and well-structured species (Figures S4B–S4C).
Protein: DP00288 (UniProt Q06253)
Region: residues 1	to 73
Annotation: disorder to order (Structural transition)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Our mechanistic model for conditional cooperativity predicts that at saturating levels of Doc, a Doc-Phd2-Doc heterotetrameric complex that is far less capable of repressing the phd/doc operon is formed. We used SAXS to characterize this complex and examine its shape and dimensions. Based on our crystal structure, we constructed a series of alternative Phd/Doc complexes with different stoichiometries (including Phd2-Doc-Phd2, Doc-Phd2-Doc, and the two possible Phd2-Doc architectures). The comparison of the experimental scattering data to the calculated scattering curves derived from these models reveals a close correspondence only to the Doc-Phd2-Doc model and very poor fits to other architectures (Table S1). The Rg (27.5 Å) calculated from the Guinier analysis and the bimodal shape and maximum dimension of the particle (Dmax = 85 Å) obtained from the distance distribution function (P(r)) all agree with our V-shaped model of the Doc-Phd2-Doc complex. Moreover the P(r) function and Kratky plot are consistent with a properly folded, homogeneous, and well-structured species (Figures S4B–S4C).
Protein: DP00288 (UniProt Q06253)
Region: residues 1	to 73
Annotation: toxin sequestering activity (Molecular function)
Evidence: experimental phenotypic evidence used in manual assertion
Supporting statements:
We further validated the role of site L in autoregulation (again in a nontoxic DocH66Y background) in vivo using a lacZ repression assay and through an indirect toxicity assay that reports the presence of a functional site H (see Extended Experimental Procedures for details). Knocking out site L is expected to result in a Doc phenotype unable to act as corepressor but still capable of binding Phd through site H. As expected, most mutants (R31A, R31D, I35A, R38A, R38D, A61W, A61D, R64E, and R64W) show a decreased corepression activity (Figure 5B; Table S5), remaining, however, capable of displacing wild-type Doc from site H. This effect is severely marked for the mutants R38D and A61D (in agreement with our in vitro results). These site L mutants disrupt the interaction of Phd with Asp53 (in the case of the R38D mutation) or introduce a negative charge in the hydrophobic pocket that accommodates residues Phe56 and Phe60 of Phd (for A61D) and results in a complete loss of corepression. However, their ability to bind Phd through their H site remains intact (Figure 5C; Table S5). Thus the low-affinity interaction that is required to establish a Doc-bridge between two operator-bound Phd dimers is crucial for Doc-mediated enhancement of repression.
Protein: DP00288 (UniProt Q06253)
Region: residues 51	to 73
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
DocH66Y was crystallized in complex with a peptide encompassing the C-terminal 22 amino acids of Phd with Se-Met substituted for Leu-52 and Leu-70 (Phd52–73Se). This fragment was chosen based upon previous work that delineates the toxin-binding domain of Phd (14, 15).
Phd52–73Se binds into a groove of DocH66Y of which helix α4 forms the base and that is flanked by helix α1 on one side and the loop α4-α5 on the other side (Fig. 1A).
Cross-references: PDB:3dd7
Protein: DP00288 (UniProt Q06253)
Region: residues 51	to 73
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows the antitoxin phd ordered when is bound to Doc.
Cross-references: PDB:3DD7
Protein: DP00288 (UniProt Q06253)
Region: residues 58	to 73
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal domain (Ala57-Arg73) of this dimer is also structured due to lattice interactions (Figure 1B; Figure S1D). The conformations adopted by the C terminus are distinct from each other and from the Doc-bound conformations (see below). They contain variable amounts of a helix and likely sample the conformational ensemble of the Phd C-terminal domain in solution.
In this case the disordered nature of the quoted region does not (only) come from missing residues but also from the large differences between the coordinates of the various copies of the protein in the crystal. This shows that some residues have resolved coordinates only because of crystal contacts, and these have been annotated as disordered as well (in line with the authors' assertion).
Cross-references: PDB:3HRY
Protein: DP00288 (UniProt Q06253)
Region: residues 51	to 73
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The PDB shows the antitoxin phd ordered when is bound to Doc.
Cross-references: PDB:3DD7
Protein: DP00288 (UniProt Q06253)
Region: residues 41	to 57
Annotation: order to disorder (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
More significantly, when we map the R2/R1 data on the X-ray structure of Phd (Figure 1F), the “dynamic hot spots” correspond to α helices α2 and α3, two regions that lose structure in the partially disordered conformation observed in the X-ray structure.
This region corresponds to α helix 3.
Cross-references: PDB:3HS2
PDB:3HRY
Protein: DP00288 (UniProt Q06253)
Region: residues 1	to 73
Annotation: negative regulation of transcription, DNA-templated (Biological process)
Evidence: beta-galactosidase reporter gene assay evidence used in manual assertion
Supporting statements:
These site L mutants disrupt the interaction of Phd with Asp53 (in the case of the R38D mutation) or introduce a negative charge in the hydrophobic pocket that accommodates residues Phe56 and Phe60 of Phd (for A61D) and results in a complete loss of corepression. However, their ability to bind Phd through their H site remains intact (Figure 5C; Table S5). Thus the low-affinity interaction that is required to establish a Doc-bridge between two operator-bound Phd dimers is crucial for Doc-mediated enhancement of repression.
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 65	to 77
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
15N{1H} NOE values less than 0.65 were observed for residues in unstructured regions (residues 65−77 and 198−211). 
Cross-references: PDB:2JUL
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 198	to 211
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
15N{1H} NOE values less than 0.65 were observed for residues in unstructured regions (residues 65−77 and 198−211). 
Cross-references: PDB:2JUL
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 65	to 256
Annotation: molten globule to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
 Mg2+ binding to DREAM-C increased the NMR chemical shift dispersion and promoted long range NOEs in the NOESY spectrum (data not shown), demonstrating that Mg2+-bound DREAM-C adopts at least some stable tertiary structure in contrast to the metal-free protein.
Significant spectral changes induced by adding Ca2+ to the Mg2+-bound protein sample indicated that Ca2+-induced conformational changes are distinct and separate from the Mg2+-induced changes (Fig. 6, B and C).
The HSQC spectrum of Ca2+/Mg2+-saturated DREAM-C exhibited variable peak intensities, suggesting exchange broadening perhaps associated with Ca2+-induced dimerization (see Fig. 5). Pulsed-field gradient diffusion NMR studies determined a hydrodynamic radius of 3.2 nm, corresponding to a stable Ca2+-bound protein dimer that persisted under a wide range of protein concentrations (0.05–1 mm).
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 65	to 256
Annotation: calcium ion binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Titration of CaCl2 into apoDREAM-C (in the absence of Mg2+) resulted in a binding isotherm that is multiphasic and could be fit by the binding of three or more Ca2+ ions, consistent with previous binding studies (10, 24). The isotherm exhibited stoichiometric binding of two Ca2+ (Kd ∼ 1–10 μm) followed by endothermic binding of one or more Ca2+ ion(s) with much lower affinity.
The presence of physiological levels of Mg2+ (5 mm Mg2+) had a profound affect on the ITC Ca2+ binding isotherms of wild-type and EF-hand mutants (Fig. 3B). The Ca2+ binding isotherm of wild-type in the presence of physiological Mg2+ was saturated with a Ca2+ binding stoichiometry of two, in contrast to a stoichiometry of three in the absence of Mg2+ (Fig. 3A).
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 139	to 150
Annotation: calcium ion binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
To simplify the analysis, we have constructed various single-site mutants that disable functional Ca2+ binding to the individual EF-hands (Fig. 1): D150N (EF-2), E186Q (EF-3), and E234Q (EF-4). In each mutant, a negatively charged Glu or Asp at the 12-position in the EF-hand loop has been substituted with a corresponding neutral residue (Gln or Asn) that dramatically lowers the Ca2+ binding affinity of the respective EF-hand outside of the physiological range of Ca2+ (31, 32).
In summary, EF-2 is an endothermic site with low affinity that gives rise to the non-stoichiometric binding in the wild-type isotherm. EF-3 and EF-4 are relatively high affinity sites (stoichiometric binding) whose enthalpies nearly cancel one another in the wild-type isotherm.
The authors refers to the 139-150 region as EF-2.
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 175	to 186
Annotation: calcium ion binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
To simplify the analysis, we have constructed various single-site mutants that disable functional Ca2+ binding to the individual EF-hands (Fig. 1): D150N (EF-2), E186Q (EF-3), and E234Q (EF-4). In each mutant, a negatively charged Glu or Asp at the 12-position in the EF-hand loop has been substituted with a corresponding neutral residue (Gln or Asn) that dramatically lowers the Ca2+ binding affinity of the respective EF-hand outside of the physiological range of Ca2+ (31, 32).
In summary, EF-2 is an endothermic site with low affinity that gives rise to the non-stoichiometric binding in the wild-type isotherm. EF-3 and EF-4 are relatively high affinity sites (stoichiometric binding) whose enthalpies nearly cancel one another in the wild-type isotherm.
The authors refers to the 175-186 region as EF-3.
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 223	to 234
Annotation: calcium ion binding (Molecular function)
Evidence: loss-of-function mutant phenotype evidence used in manual assertion
Supporting statements:
To simplify the analysis, we have constructed various single-site mutants that disable functional Ca2+ binding to the individual EF-hands (Fig. 1): D150N (EF-2), E186Q (EF-3), and E234Q (EF-4). In each mutant, a negatively charged Glu or Asp at the 12-position in the EF-hand loop has been substituted with a corresponding neutral residue (Gln or Asn) that dramatically lowers the Ca2+ binding affinity of the respective EF-hand outside of the physiological range of Ca2+ (31, 32).
In summary, EF-2 is an endothermic site with low affinity that gives rise to the non-stoichiometric binding in the wild-type isotherm. EF-3 and EF-4 are relatively high affinity sites (stoichiometric binding) whose enthalpies nearly cancel one another in the wild-type isotherm.
The authors refers to the 223-234 region as EF-4.
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 65	to 256
Annotation: magnesium ion binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
Analysis of the binding isotherm using a “two sites” model (Microcal Origin software) revealed that DREAM-C has one Mg2+ site with relatively high affinity (dissociation constant of 13 μm and ΔH = -0.79 kcal/mol), and two or more sites with much lower affinity (Kd in the millimolar range and ΔH = +3.97 kcal/mol).
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 65	to 256
Annotation: protein homodimerization activity (Molecular function)
Evidence: gel-filtration evidence used in manual assertion
Supporting statements:
By contrast, Ca2+-saturated DREAM-C in the presence of Mg2+ eluted with an apparent molecular mass of 50 kDa in solution (Fig. 5), indicating that the Ca2+-bound protein forms a stable dimer even at very dilute protein concentrations (10). Similar calcium-sensitive hydrodynamic properties were observed for each of the EF-hand mutants (data not shown), suggesting that each mutant is structurally intact. In summary, DREAM-C appears to be a monomer under basal physiological conditions (5 mm Mg2+ and 100 nm Ca2+) and forms a stable dimer at saturating Ca2+ levels.
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 65	to 256
Annotation: molten globule (Structural state)
Evidence: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion
Supporting statements:
The poor chemical shift dispersion demonstrates that apoDREAM-C adopts an unstructured molten-globule state similar to that described for apo states of many other EF-hand proteins (30, 34, 35).
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 65	to 256
Annotation: transcription cis-regulatory region binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
Electrophoresis mobility shift assays (EMSA) were performed on the EF-hand mutants to monitor their Ca2+-sensitive binding to duplex oligonucleotide derived from the downstream response element (DRE) of the prodynorphin gene (Fig. 7).
A typical EMSA for DREAM is shown in Fig. 7 and exhibits two shifted bands that represent different oligomeric species of DREAM bound to DRE.
In summary, Mg2+ is required for sequence-specific binding to DRE and Ca2+ binding at either EF-3 or EF-4 is sufficient to abolish DNA binding.
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 223	to 234
Annotation: negative regulation of DNA binding (Biological process)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
In summary, Mg2+ is required for sequence-specific binding to DRE and Ca2+ binding at either EF-3 or EF-4 is sufficient to abolish DNA binding.
A second implication of this study is that Ca2+ binding at EF-3 and EF-4 promotes protein dimerization that somehow disrupts DNA binding by DREAM.
The authors refers to the 223-234 region as EF-4.
Protein: DP00291 (UniProt Q9QXT8)
Region: residues 175	to 186
Annotation: negative regulation of DNA binding (Biological process)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
In summary, Mg2+ is required for sequence-specific binding to DRE and Ca2+ binding at either EF-3 or EF-4 is sufficient to abolish DNA binding.
A second implication of this study is that Ca2+ binding at EF-3 and EF-4 promotes protein dimerization that somehow disrupts DNA binding by DREAM.
The authors refers to the 175-186 region as EF-3.
Protein: DP00292 (UniProt P0C5S4)
Region: residues 85	to 97
Annotation: disorder (Structural state)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
There are few NOEs for residues 85–97, which connect helices αD and αE.
Cross-references: PDB:1Y6D
Protein: DP00298 (UniProt Q07817)
Region: residues 28	to 80
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
This observation suggests that, in the absence of IDR post-translational modifications, the α1-α2 IDR transiently interacts in cis with the folded core of Bcl-xL
(NOE) spectra for Bcl-xL with the S62E phosphomimetic mutation showed that residues within the α1-α2 IDR exhibited reduced flexibility in comparison to wild-type Bcl-xL
Protein: DP00298 (UniProt Q07817)
Region: residues 25	to 80
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We used this construct for NMR experiments because intense resonances of the disordered loop overlap and interfere with those of the folded BCL-xL core. The α1-α2 loop was, however, present in the BCL-xLΔC construct, lacking only the C-terminal 22 residues18, used for other functional assays.
The PDB structure shows this region lacks electron density, indicating it is disordered.
Cross-references: PDB:4HNJ
Protein: DP00299 (UniProt P0AE70)
Region: residues 16	to 29
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates 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
Substrate Binding Folds an Otherwise Disordered Substratebinding Loop of EcMazF. Most loop regions are well structured, with exception of loops 1-2 (residues Asp-16– Arg-29) and 4-5 (residues Leu-64–Gly-71) (Fig. 1C). 

Cross-references: PDB:5CKB
PDB:5CO7
PDB:5CK9
Protein: DP00299 (UniProt P0AE70)
Region: residues 16	to 29
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
Substrate Binding Folds an Otherwise Disordered Substratebinding Loop of EcMazF. Most loop regions are well structured, with exception of loops 1-2 (residues Asp-16– Arg-29) and 4-5 (residues Leu-64–Gly-71) (Fig. 1C). [...] The crystal structure of EcMazF in complex with the substrate-mimicking DNA sequence d(A1 U2 A3 C4 A5 U6 A7 ) (from now on referred to as “substrate complex”) was determined at 3.0 Å resolution (Table 1).. Loops 1-2 and 4-5 are fully ordered and adopt identical conformations in all three monomers


Cross-references: PDB:5CR2
PDB:5CQY
PDB:5CQX
Protein: DP00299 (UniProt P0AE70)
Region: residues 16	to 29
Annotation: molecular function activator 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
Substrate Binding Folds an Otherwise Disordered Substratebinding Loop of EcMazF. Most loop regions are well structured, with exception of loops 1-2 (residues Asp-16– Arg-29) and 4-5 (residues Leu-64–Gly-71) (Fig. 1C). [...] The crystal structure of EcMazF in complex with the substrate-mimicking DNA sequence d(A1 U2 A3 C4 A5 U6 A7 ) (from now on referred to as “substrate complex”) was determined at 3.0 Å resolution (Table 1).. Loops 1-2 and 4-5 are fully ordered and adopt identical conformations in all three monomers


Both EcMazF and BsMazF only adapt a catalytically competent conformation for loop 1-2 when a substrate or substrate mimic is bound (27). In both enzymes, the antitoxin also prevents loop 1-2 from adopting this conformation. 
Ordering of the loops occurs only upon binding the substrate, bringing about the catalytically active form
Cross-references: PDB:5CR2
PDB:5CQY
PDB:5CQX