LiteFold/DisProt huggingface dataset:
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: disorder to order (Structural transition)
Evidence: spectrometry evidence used in manual assertion
Supporting statements:
These observations support a CysCysHisCys ligand configuration for the NZF1-type zinc binding domains, indicating that one of the conserved histidines is involved in metal ion binding whereas the other plays some other as-yet-undetermined role.
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: DNA binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Metal-stabilized structured regions were identified by partial proteolysis and examined for binding to the β-retinoic acid response element (β-RARE).
In the presence of zinc, multiple bands were observed at early time points. By 1 h, the major products were two fragments of approximately 10 kDa each. These were stable for up to 3 h of digestion.
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: DNA binding (Molecular function)
Evidence: DNAse footprinting evidence used in manual assertion
Supporting statements:
DNase I footprinting was used to further characterize the DNA binding site.
Gel shift analysis with the β-RARE DNA binding site showed that both fragments are functional DNA binding domains.
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: zinc ion binding (Molecular function)
Evidence: spectrometry evidence used in manual assertion
Supporting statements:
These observations support a CysCysHisCys ligand configuration for the NZF1-type zinc binding domains, indicating that one of the conserved histidines is involved in metal ion binding whereas the other plays some other as-yet-undetermined role.
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: zinc ion binding (Molecular function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The cobalt(II) and zinc(II) binding properties of the metal binding domains were investigated, and zinc-induced protein folding was observed by 1H NMR.
Titration of zinc(II) into the apoprotein led to dispersion of these resonances, indicative of structure formation.
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: zinc ion binding (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Metal-stabilized structured regions were identified by partial proteolysis and examined for binding to the β-retinoic acid response element (β-RARE).
In the presence of zinc, multiple bands were observed at early time points. By 1 h, the major products were two fragments of approximately 10 kDa each. These were stable for up to 3 h of digestion.
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: metal ion sequestering activity (Molecular function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Metal-stabilized structured regions were identified by partial proteolysis and examined for binding to the β-retinoic acid response element (β-RARE).
In the presence of zinc, multiple bands were observed at early time points. By 1 h, the major products were two fragments of approximately 10 kDa each. These were stable for up to 3 h of digestion.
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: metal ion sequestering activity (Molecular function)
Evidence: spectrometry evidence used in manual assertion
Supporting statements:
These observations support a CysCysHisCys ligand configuration for the NZF1-type zinc binding domains, indicating that one of the conserved histidines is involved in metal ion binding whereas the other plays some other as-yet-undetermined role.
Protein: DP00049 (UniProt P70475)
Region: residues 487	to 606
Annotation: metal ion sequestering activity (Molecular function)
Evidence: proton-based nuclear magnetic resonance evidence used in manual assertion
Supporting statements:
The cobalt(II) and zinc(II) binding properties of the metal binding domains were investigated, and zinc-induced protein folding was observed by 1H NMR.
Titration of zinc(II) into the apoprotein led to dispersion of these resonances, indicative of structure formation.
Protein: DP00049 (UniProt P70475)
Region: residues 90	to 172
Annotation: disorder (Structural state)
Evidence: curator inference from database used in manual assertion
Supporting statements:
This poly-E region is inferred by the curator to be disordered, based on MobiDB-Lite and according to experimental evidence demonstrating that poly-E repeats display random-coil-like conformation (PMID:16949547)
Protein: DP00051 (UniProt P07805)
Region: residues 1	to 32
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the electron density map for most of the residues is unambiguous, 70 residues could not be interpreted. These regions include the N-terminus (residues 1−35), the C-terminus (residues 412−425), and two loops (residues 158−165 and 298−310).
Cross-references: PDB:2TOD
PDB:1QU4
Protein: DP00051 (UniProt P07805)
Region: residues 296	to 308
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the electron density map for most of the residues is unambiguous, 70 residues could not be interpreted. These regions include the N-terminus (residues 1−35), the C-terminus (residues 412−425), and two loops (residues 158−165 and 298−310).
Cross-references: PDB:2TOD
PDB:1QU4
Protein: DP00051 (UniProt P07805)
Region: residues 410	to 423
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the electron density map for most of the residues is unambiguous, 70 residues could not be interpreted. These regions include the N-terminus (residues 1−35), the C-terminus (residues 412−425), and two loops (residues 158−165 and 298−310).
Cross-references: PDB:2TOD
PDB:1QU4
Protein: DP00051 (UniProt P07805)
Region: residues 410	to 423
Annotation: flexible C-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the electron density map for most of the residues is unambiguous, 70 residues could not be interpreted. These regions include the N-terminus (residues 1−35), the C-terminus (residues 412−425), and two loops (residues 158−165 and 298−310).
Cross-references: PDB:2TOD
PDB:1QU4
Protein: DP00051 (UniProt P07805)
Region: residues 1	to 32
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the electron density map for most of the residues is unambiguous, 70 residues could not be interpreted. These regions include the N-terminus (residues 1−35), the C-terminus (residues 412−425), and two loops (residues 158−165 and 298−310).
Cross-references: PDB:2TOD
PDB:1QU4
Protein: DP00053 (UniProt P27001)
Region: residues 1	to 101
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The sequence from Thermus thermophilus HB8 described in this article (Q5SGX2) is 100% identical to P27001.
The most pronounced difference between the two states is the ordering of the N-terminal region of the α subunit, which appeared to comprise a coiled-coil structure (helical arm). The helices stretch out into the solvent by 65 Å and are apparently flexible in the absence of intermolecular contacts.
Protein: DP00053 (UniProt P27001)
Region: residues 1	to 101
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The sequence from Thermus thermophilus HB8 described in this article (Q5SGX2) is 100% identical to P27001.
The most pronounced difference between the two states is the ordering of the N-terminal region of the α subunit, which appeared to comprise a coiled-coil structure (helical arm). The helices stretch out into the solvent by 65 Å and are apparently flexible in the absence of intermolecular contacts.
Cross-references: PDB:1EIY
Protein: DP00053 (UniProt P27001)
Region: residues 1	to 84
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1-84 from the amino-terminus of the α-subunit are disordered and were not detected in the electron density maps.
The sequence from Thermus thermophilus HB8 described in this article (Q5SGX2) is 100% identical to P27001.
Cross-references: PDB:1PYS
Protein: DP00053 (UniProt P27001)
Region: residues 1	to 84
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1-84 from the amino-terminus of the α-subunit are disordered and were not detected in the electron density maps.
The sequence from Thermus thermophilus HB8 described in this article (Q5SGX2) is 100% identical to P27001.
Protein: DP00053 (UniProt P27001)
Region: residues 1	to 101
Annotation: tRNA binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The sequence from Thermus thermophilus HB8 described in this article (Q5SGX2) is 100% identical to P27001.
The most pronounced difference between the two states is the ordering of the N-terminal region of the α subunit, which appeared to comprise a coiled-coil structure (helical arm). The helices stretch out into the solvent by 65 Å and are apparently flexible in the absence of intermolecular contacts.
Cross-references: PDB:1EIY
Protein: DP00054 (UniProt P78356)
Region: residues 1	to 33
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal 33 amino acids are completely disordered.
Cross-references: PDB:1BO1
Protein: DP00054 (UniProt P78356)
Region: residues 304	to 342
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 304–342, which comprise the central portion of the highly variable insert sequence, are disordered.
Cross-references: PDB:1BO1
Protein: DP00054 (UniProt P78356)
Region: residues 373	to 390
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Finally, the Lys- and Ala-rich loop from 373–390 is disordered. This loop connects the C terminus of β12 to the N terminus of α8, a distance of 22 Å.
Cross-references: PDB:1BO1
Protein: DP00055 (UniProt P10688)
Region: residues 133	to 157
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Due to missing electron density, no structural model was possible for these residues.
Cross-references: PDB:1DJW
PDB:1DJY
PDB:1DJX
PDB:1DJZ
Protein: DP00055 (UniProt P10688)
Region: residues 446	to 483
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Due to missing electron density, no structural model was possible for these residues.
Cross-references: PDB:1DJW
PDB:1DJY
PDB:1DJX
PDB:1DJZ
Protein: DP00057 (UniProt P15340)
Region: residues 1	to 62
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
CD spectra showed that the fowl protamine, galline, has an unordered structure rich in reverse turns in neutral solution.
In ET buffer, the spectrum had a positive peak at 224 nm besides a trough near 200 nm. The former peak is probably due to a reverse turn (β-turn) structure (19, 20) and the latter one to an unordered structure (19, 21).
Protein: DP00057 (UniProt P15340)
Region: residues 1	to 62
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Citrate ions bound specifically to the galline molecule, causing a conformational change in it.
In fact, [θ224] decreased with an increase in citrate concentration (Fig. 1B).
Protein: DP00057 (UniProt P15340)
Region: residues 1	to 62
Annotation: carboxylic acid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Citrate ions bound specifically to the galline molecule, causing a conformational change in it.
In fact, [θ224] decreased with an increase in citrate concentration (Fig. 1B).
Protein: DP00057 (UniProt P15340)
Region: residues 1	to 62
Annotation: DNA binding (Molecular function)
Evidence: static light scattering assay evidence used in manual assertion
Supporting statements:
Spectrophotometric analyses revealed that galline efficiently bound to DNA in 0.25mM EDTA/10mM Tricine-HC1, pH 7.4, but hardly so in 30mM NaC1/3mM sodium citrate, pH7.0.
Spectrophotometric analyses showed that galline bound efficiently to DNA in ET buffer, but hardly so in 0.2 X SSC.
Protein: DP00060 (UniProt P11409)
Region: residues 179	to 216
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In   both   molecules   ∼40   amino   acids (Pro179–Gly216), located immediately after strand β7 and before strand β8, were not modeled in the current structure because of poor electron density. This poor density suggests that these aminoacids are very flexible.
The dashed line indicates a flexible region (amino acids 179–216) which is not modeled in the current structure.
Cross-references: PDB:1BOO
Protein: DP00061 (UniProt P27694)
Region: residues 109	to 168
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Human replication protein A: global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible C-terminal linker
We have solved the global fold of the fragment corresponding to this domain (RPA70 delta 169) and we find residues 8-108 of the N-terminal domain are structured. The remaining C-terminal residues are unstructured and may form a flexible linker to the DNA-binding domain of RPA70.
A heteronuclear 15N-1H NOE spectrum labeled with assigned resonances from the C-terminal linker region. All labeled resonances are negative relative to a control spectrum, indicating fast internal backbone motion in the linker. Almost all other unlabeled resonances are also negative and not from the globular region, we assume they are also from the linker.
The longest (1665 ms) time point of the 15N-T1 experiment shows that the resonances in (a) also have long 15N-T1’s; another strong indication that the C-terminus is flexible
The N-terminal 8–108 amino acid residues form a five-stranded β-barrel capped on both ends by short helices. A 60 residue long flexible segment links the structured domain with the tandem DNA-binding domains of RPA70.
Protein: DP00061 (UniProt P27694)
Region: residues 109	to 168
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Human replication protein A: global fold of the N-terminal RPA-70 domain reveals a basic cleft and flexible C-terminal linker
We have solved the global fold of the fragment corresponding to this domain (RPA70 delta 169) and we find residues 8-108 of the N-terminal domain are structured. The remaining C-terminal residues are unstructured and may form a flexible linker to the DNA-binding domain of RPA70.
A heteronuclear 15N-1H NOE spectrum labeled with assigned resonances from the C-terminal linker region. All labeled resonances are negative relative to a control spectrum, indicating fast internal backbone motion in the linker. Almost all other unlabeled resonances are also negative and not from the globular region, we assume they are also from the linker.
The longest (1665 ms) time point of the 15N-T1 experiment shows that the resonances in (a) also have long 15N-T1’s; another strong indication that the C-terminus is flexible
The N-terminal 8–108 amino acid residues form a five-stranded β-barrel capped on both ends by short helices. A 60 residue long flexible segment links the structured domain with the tandem DNA-binding domains of RPA70.
Protein: DP00061 (UniProt P27694)
Region: residues 105	to 180
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation
The IULD functions to tether two high affinity single stranded DNA binding domains (DBD A and B) to an N-terminal single stranded DNA (ssDNA) binding and protein interaction domain (DBD F; see Fig. 1 for domain structure of RPA70) (Daughdrill et al. 2001).
Plot showing the values for the reduced spectral density function at 0 frequency, J(0). J(0) values are plotted on the vertical axis and residue number is plotted on the horizontal axis. 
Unstructured linker domain (IULD) connecting two compact globular regions - the N-terminal DBD F domain and the ss-DNA binding DBD A domain - in the 70 kDa subunit of replication protein A (RPA70).
Protein: DP00061 (UniProt P27694)
Region: residues 105	to 180
Annotation: flexible linker (Disorder function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Dynamic Behavior of an Intrinsically Unstructured Linker Domain Is Conserved in the Face of Negligible Amino Acid Sequence Conservation
The IULD functions to tether two high affinity single stranded DNA binding domains (DBD A and B) to an N-terminal single stranded DNA (ssDNA) binding and protein interaction domain (DBD F; see Fig. 1 for domain structure of RPA70) (Daughdrill et al. 2001).
Plot showing the values for the reduced spectral density function at 0 frequency, J(0). J(0) values are plotted on the vertical axis and residue number is plotted on the horizontal axis.
Unstructured linker domain (IULD) connecting two compact globular regions - the N-terminal DBD F domain and the ss-DNA binding DBD A domain - in the 70 kDa subunit of replication protein A (RPA70).
Protein: DP00062 (UniProt P19793)
Region: residues 1	to 130
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
For the NTD–DBD–DNA complex, the representative ensemble shown in Figure 4E is in agreement with NMR data indicating a highly disordered and flexible domain.
Overall, these data demonstrate a high degree of flexibility of the NTDs that is restrained by the space occupied by the hinge and LBD dimer in the context of the full-length protein.
Protein: DP00062 (UniProt P19793)
Region: residues 1	to 130
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Experimental evidence of the disordered state of the RXRα NTD was provided by liquid state NMR.
These observations suggest that the RXRα NTD is disordered in solution.
Protein: DP00062 (UniProt P19793)
Region: residues 178	to 187
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The {1H}-15N NOEs  show that residues 178 to 187 clearly exhibit smaller than average NOE values, indicating increased flexibility in this region.
Cross-references: PDB:1RXR
Protein: DP00062 (UniProt P19793)
Region: residues 178	to 187
Annotation: zinc ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The second zinc ion is complexed by cysteine residues 171, 177, 187 and 190, forming a second zinc loop.
Cross-references: PDB:1RXR
Protein: DP00062 (UniProt P19793)
Region: residues 169	to 189
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The non-helical regions of the structure are less well-ordered, in particular the region between the first and second helix, residues 169 to 189.
Cross-references: PDB:1RXR
Protein: DP00063 (UniProt P49799)
Region: residues 1	to 50
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Iterative rounds of four-fold noncrystallographic symmetry (NCS) averaging, solvent flattening, and electron density map interpretation yielded a model comprising 128 residues of RGS4 and virtually all of the Giα1 subunit.
The current model of RGS4–Giα1 contains two molecules of Giα1 (chain A, residues 5–354; chain D, residues 11–354), two molecules of RGS4 (chain E, residues 51–178; chain H, residues 60–175), two citrate ions, and 56 water molecules.
Accordingly, the arms of RGS4 are disordered and play no obvious role either in binding Giα1 or in stabilizing the RGS box.
Cross-references: PDB:1AGR
Protein: DP00063 (UniProt P49799)
Region: residues 179	to 205
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Iterative rounds of four-fold noncrystallographic symmetry (NCS) averaging, solvent flattening, and electron density map interpretation yielded a model comprising 128 residues of RGS4 and virtually all of the Giα1 subunit.
The current model of RGS4–Giα1 contains two molecules of Giα1 (chain A, residues 5–354; chain D, residues 11–354), two molecules of RGS4 (chain E, residues 51–178; chain H, residues 60–175), two citrate ions, and 56 water molecules.
Accordingly, the arms of RGS4 are disordered and play no obvious role either in binding Giα1 or in stabilizing the RGS box.
Cross-references: PDB:1AGR
Protein: DP00064 (UniProt P03607)
Region: residues 20	to 57
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1 to 38 are disordered and buried in the RNA in all subunits. Residues 39 to 62 are ordered only in the C subunit.
Cross-references: PDB:4SBV
Protein: DP00065 (UniProt O86488)
Region: residues 569	to 1123
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
However, on a TSK gel filtration column equilibrated in buffer A containing 1 mm EGTA or 1 mm Ca2+, it eluted with apparent molecular masses of 320 and 250 kDa, respectively.
Protein: DP00065 (UniProt O86488)
Region: residues 569	to 1123
Annotation: calcium ion binding (Molecular function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Equilibrium gel filtration experiments at low (10 mm Tris-HCl, pH 7.5) as well as moderately high ionic strength (50 mm Tris-HCl, pH 7.5, 150 mm KCl) and a free Ca2+ concentration of 40–60 μm showed that B1–B5 binds 14–15 mol of Ca2+/mol, which seems to be a very good estimation of the total capacity.