LiteFold/DisProt huggingface dataset:
Protein: DP02630 (UniProt O14958)
Region: residues 371	to 399
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the crystal structure, two N-terminal residues and 29 C-terminal residues starting from N371 are disordered and the corresponding electron densities for these regions are not visible
Cross-references: PDB:2VAF
Protein: DP02630 (UniProt O14958)
Region: residues 371	to 399
Annotation: phosphorylation display site (Disorder function)
Evidence: protein mass spectrometry evidence used in manual assertion
Supporting statements:
Therefore, Ser385 and Ser393, which had been confirmed by the mass spectroscopy as the phosphorylation sites, were mutated to aspartic acids to mimic the charge and length of the phosphoserine residue.
However, the MALDI mass spectroscopy data have indicated, without ambiguity, that the phosphorylation sites on hCASQ2 are Ser385 and Ser393, but not Thr372.
In addition, the back-to-back interface has the polyanionic C-terminal disordered tail in it, which is composed of residues from 371 to 399 in the case of hCASQ2. Thus, this disordered tail contains both phosphorylation sites, Ser385 and Ser393 (Fig. 7). The twenty-six out of twenty-nine residues in the disordered C-terminus of hCASQ2 are acidic residues.
Protein: DP02630 (UniProt O14958)
Region: residues 371	to 399
Annotation: disorder to order (Structural transition)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
In addition, small angle X-ray scattering determined that in high concentrations of Ca2+, S385D:S393D exists in more compact forms of oligomer than those of unphosphorylated hCASQ2 (Fig. 5a, b). Therefore, the disorder-order transition through phosphorylation-induced helix formation delays Ca2+-dependent aggregation probably through providing more stable back-to-back interface.
Therefore, phosphorylation of two serine residues in the highly acidic C-terminal tail increases not only the negative charge in the back-to-back interface, but also establishes a disorder-order transition through the formation of extra-helices and tight interaction with existing positive patches.
The authors report the exact phosphorylation sites of hCASQ2 for the first time. It was also showed that phosphoserine mimicking double mutant of hCASQ2 has a substantial increase in its Ca2+ binding capacity, solubility and α-helix content, probably due to the extra negative charge and order-disorder transition in the back-to-back interface.
Protein: DP02630 (UniProt O14958)
Region: residues 371	to 399
Annotation: calcium ion sequestering activity (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
In the crystal structures of both CASQ1 and CASQ2 from various species [20, 39, 46], two distinct dimerization contacts are observed: front-to-front and back-to-back, which involve the N-terminal and C-terminal residues, respectively. Those interfaces form the basis of dimer, tetramer, and possibly further polymers of CASQ. Not only do the observed polymers have the morphology inferred for the physiologically relevant aggregation [23], but these two interfaces also provide the basis for a mechanism to couple Ca2+-binding and polymerization
Protein: DP02630 (UniProt O14958)
Region: residues 371	to 399
Annotation: calcium ion binding (Molecular function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
In the crystal structures of both CASQ1 and CASQ2 from various species [20, 39, 46], two distinct dimerization contacts are observed: front-to-front and back-to-back, which involve the N-terminal and C-terminal residues, respectively. Those interfaces form the basis of dimer, tetramer, and possibly further polymers of CASQ. Not only do the observed polymers have the morphology inferred for the physiologically relevant aggregation [23], but these two interfaces also provide the basis for a mechanism to couple Ca2+-binding and polymerization
In addition, the experimental approach with equilibrium dialysis and atomic absorption spectroscopy shows that the hCASQ2 double mutant shows a similar Ca2+ binding capacity up to a Ca2+-concentration of ~6–7 mM (Fig. 6). Above this Ca2+ concentration, S385D:S393D displays significantly increased Ca2+-binding capacity (Fig. 6). Coincidently, the bifurcation point of Ca2+ concentration between double mutant and others in turbidity assay (Fig. 4) is similar to that of Ca2+-binding capacity curve
Protein: DP02631 (UniProt Q39026)
Region: residues 215	to 224
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The MPK6 crystals contain two protein chains in the asymmetric unit. Amino acid residues 70–75 (part of the glycine-rich loop), 213–214 (part of the phosphorylation lip), and 366–374 (part of the L16 loop) in chain A and amino acid residues 215–224 (phosphorylation lip) and 285–287 (part of the MAPK insert) in chain B were not resolved in the electron density maps.
Cross-references: PDB:5CI6
Protein: DP02631 (UniProt Q39026)
Region: residues 215	to 224
Annotation: phosphorylation display site (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The MPK6 crystals contain two protein chains in the asymmetric unit. Amino acid residues 70–75 (part of the glycine-rich loop), 213–214 (part of the phosphorylation lip), and 366–374 (part of the L16 loop) in chain A and amino acid residues 215–224 (phosphorylation lip) and 285–287 (part of the MAPK insert) in chain B were not resolved in the electron density maps.
Cross-references: PDB:5CI6
Protein: DP02632 (UniProt P31321)
Region: residues 59	to 81
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although 21 residues of the linker region between the D/D domain and the CNB-A domain of each R-subunit (residues 59–81) are still missing in our structure, several features are clear.
Cross-references: PDB:4DIN
Protein: DP02632 (UniProt P31321)
Region: residues 59	to 81
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although 21 residues of the linker region between the D/D domain and the CNB-A domain of each R-subunit (residues 59–81) are still missing in our structure, several features are clear.
The unusual feature of our structure was that we were capable to visualize both the D/D domain and the CNB domains simultaneously. Structures of these domains for different R-subunits were solved previously only separately. The extended flexible linker between these domains prevented crystallization of the full length R-subunits. 
The entire linker segment that joins the D/D domain to CNB-A is classified as an intrinsic disordered region, and embedded within this segment is the inhibitor site (IS) that docks to the active site cleft of the C-subunit in the holoenzyme. 
Cross-references: PDB:4DIN
Protein: DP02632 (UniProt P31321)
Region: residues 1	to 13
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:4DIN
Protein: DP02633 (UniProt P22605)
Region: residues 454	to 481
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density was observed for only 10 residues (out of 40) of the RARβ C-terminal F region.
Like other members of the nuclear receptor superfamily, retinoid receptors are modular and include an N-terminal A/B activation domain, a central DNA-binding domain (region C), a linker region D, a ligand-binding domain (region E), and a C-terminal region F of unknown structure and function.
Cross-references: PDB:1XDK
Protein: DP02633 (UniProt P22605)
Region: residues 180	to 209
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density was observed for only 10 residues (out of 40) of the RARβ C-terminal F region.
Like other members of the nuclear receptor superfamily, retinoid receptors are modular and include an N-terminal A/B activation domain, a central DNA-binding domain (region C), a linker region D, a ligand-binding domain (region E), and a C-terminal region F of unknown structure and function.
Helix H2, the connection between H2 and H3 in RXRα, the D-region and the last 30 residues of the F-region in RARβ, could not be modeled due to poor electron density in these regions.
Cross-references: PDB:1XDK
Protein: DP02633 (UniProt P22605)
Region: residues 180	to 209
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Electron density was observed for only 10 residues (out of 40) of the RARβ C-terminal F region.
Like other members of the nuclear receptor superfamily, retinoid receptors are modular and include an N-terminal A/B activation domain, a central DNA-binding domain (region C), a linker region D, a ligand-binding domain (region E), and a C-terminal region F of unknown structure and function.
Helix H2, the connection between H2 and H3 in RXRα, the D-region and the last 30 residues of the F-region in RARβ, could not be modeled due to poor electron density in these regions.
Cross-references: PDB:1XDK
Protein: DP02634 (UniProt Q9UBV7)
Region: residues 260	to 285
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In B, the long loop region, residues 260–285, invisible in the open conformation, is highlighted in red.
In the open conformation crystal structure (Fig. 1A), no electron density was observed for a region encompassing residues 260–278, and only weak backbone electron density could be traced for residues 278–284. 
In the crystal structures of human β4GalT7, the missing and weak electron
density from residues 260–284, together with the presence of the Trp224 side chain rotamers in the open conformation (data not shown), suggest structural flexibility in this region.
In the open conformation (A), the electron density was visible up to His259 , and the clear electron density appeared again at Gly285 (blue sphere). 
Cross-references: PDB:4IRP
Protein: DP02634 (UniProt Q9UBV7)
Region: residues 260	to 285
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the open conformation crystal structure (Fig. 1A), no electron density was observed for a region encompassing residues 260–278, and only weak backbone electron density could be traced for residues 278–284. In contrast, the same region in the closed conformation had clear electron density corresponding to a long loop, residues 260–285 (Fig. 1B). The appearance of the long loop coincides with the change in the orientation of the Trp224 side chain, from pointing away to pointing toward the binding pocket, forming a hydrogen bond with the β-phosphate oxygen atom of the bound UDP (Fig. 1B).
In the open conformation (A), the electron density was visible up to His259 , and the clear electron density appeared again at Gly285 (blue sphere). The His257 -X-His259 motif, Trp224 , and the N and C termini are indicated. A disulfide bond is shown in a ball-and-stick format, with the yellow spheres indicating sulfur atoms. In B, the long loop region, residues 260 –285, invisible in the open conformation, is highlighted in red.
Cross-references: PDB:4IRP
PDB:4IRQ
Protein: DP02634 (UniProt Q9UBV7)
Region: residues 260	to 285
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We present here the crystal structures of human β4GalT7 in open and closed conformations. A comparison of these crystal structures shows that, upon
manganese and UDP or UDP-Gal binding, the enzyme undergoes conformational changes involving a small and a long loop.
In the open conformation crystal structure (Fig. 1A), no electron density was observed for a region encompassing residues 260–278, and only weak backbone electron density could be traced for residues 278–284. In contrast, the same region in the closed conformation had clear electron density corresponding to a long loop, residues 260–285 (Fig. 1B). The appearance of the long loop coincides with the change in the orientation of the Trp224 side chain, from pointing away to pointing toward the binding pocket, forming a hydrogen bond with the β-phosphate oxygen atom of the bound UDP (Fig. 1B).
The present human β4GalT7 crystal structures show that the β4GalT7 enzyme undergoes conformational changes upon binding with manganese and UDP or UDP-Gal. This conformational change involves small and long loops containing residues Gly223-Trp224 and His259 to Gly284, respectively.
Cross-references: PDB:4IRP
Protein: DP02634 (UniProt Q9UBV7)
Region: residues 260	to 285
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the open conformation crystal structure (Fig. 1A), no electron density was observed for a region encompassing residues 260–278, and only weak backbone electron density could be traced for residues 278–284. In contrast, the same region in the closed conformation had clear electron density corresponding to a long loop, residues 260–285 (Fig. 1B). The appearance of the long loop coincides with the change in the orientation of the Trp224 side chain, from pointing away to pointing toward the binding pocket, forming a hydrogen bond with the β-phosphate oxygen atom of the bound UDP (Fig. 1B).
In the crystal structures of human β4GalT7, the missing and weak electron density from residues 260 –284, together with the presence of the Trp224 side chain rotamers in the open conformation (data not shown), suggest structural flexibility in this region.
Cross-references: PDB:4IRQ
Protein: DP02635 (UniProt Q9ERE3)
Region: residues 126	to 160
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two CISK-PX fragments were used for the crystallographic studies. One contained the PX domain (short-PX, residues 7–126) and another contained both the PX domain and the linker between the PX domain and kinase domain (long-PX, residues 7–160)
The density for this linker region, however, cannot be observed in the electron density map, which indicates that the linker region is much more dynamic compared with the PX domain in the crystallized CISK fragment. Our DLS data on different fragments of CISK-PX have shown that the fragment containing only the PX domain (residues 7–126, 14.34 kDa) is monomeric (DLS molecular mass, 16.68 kDa), whereas the fragment containing the PX domain and the linker region (residues 7–160, 18.00 kDa) is in an oligomeric form with DLS molecular weight around a dimer (35.14 kDa).
Cross-references: PDB:1XTE
Protein: DP02635 (UniProt Q9ERE3)
Region: residues 126	to 160
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two CISK-PX fragments were used for the crystallographic studies. One contained the PX domain (short-PX, residues 7–126) and another contained both the PX domain and the linker between the PX domain and kinase domain (long-PX, residues 7–160)
The density for this linker region, however, cannot be observed in the electron density map, which indicates that the linker region is much more dynamic compared with the PX domain in the crystallized CISK fragment. Our DLS data on different fragments of CISK-PX have shown that the fragment containing only the PX domain (residues 7–126, 14.34 kDa) is monomeric (DLS molecular mass, 16.68 kDa), whereas the fragment containing the PX domain and the linker region (residues 7–160, 18.00 kDa) is in an oligomeric form with DLS molecular weight around a dimer (35.14 kDa).
Nevertheless, the high tendency for CISK-PX to dimerize in the presence of the linker region implies that dimerization may play an important role in CISK membrane localization and regulation.
Furthermore, biochemical studies reveal that CISK-PX dimerizes in the presence of the linker between the PX domain and kinase domain, suggesting a multivalent mechanism in membrane localization of CISK.
Cross-references: PDB:1XTE
Protein: DP02635 (UniProt Q9ERE3)
Region: residues 126	to 160
Annotation: molecular adaptor activity (Molecular function)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Furthermore, biochemical studies reveal that CISK-PX dimerizes in the presence of the linker between the PX domain and kinase domain, suggesting a multivalent mechanism in membrane localization of CISK.
The density for this linker region, however, cannot be observed in the electron density map, which indicates that the linker region is much more dynamic compared with the PX domain in the crystallized CISK fragment. Our DLS data on different fragments of CISK-PX have shown that the fragment containing only the PX domain (residues 7–126, 14.34 kDa) is monomeric (DLS molecular mass, 16.68 kDa), whereas the fragment containing the PX domain and the linker region (residues 7–160, 18.00 kDa) is in an oligomeric form with DLS molecular weight around a dimer (35.14 kDa).
Nevertheless, the high tendency for CISK-PX to dimerize in the presence of the linker region implies that dimerization may play an important role in CISK membrane localization and regulation.
In addition to the linker region, the PX domain itself might also contribute to part of the dimer interface. At least two models exist for the dimeric state of CISK-PX. In the first model, the linker facilitates the dimerization via linker-linker interaction; in the other model, the linker from one CISK molecule interacts with another CISK-PX domain
Cross-references: PDB:1XTE
Protein: DP02635 (UniProt Q9ERE3)
Region: residues 126	to 160
Annotation: localization (Biological process)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Furthermore, biochemical studies reveal that CISK-PX dimerizes in the presence of the linker between the PX domain and kinase domain, suggesting a multivalent mechanism in membrane localization of CISK.
Nevertheless, the high tendency for CISK-PX to dimerize in the presence of the linker region implies that dimerization may play an important role in CISK membrane localization and regulation.
Cross-references: PDB:1XTE
Protein: DP02636 (UniProt O88393)
Region: residues 730	to 744
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the murine 2.7 Å crystal structure that we are presenting here, the FG-loop is disordered, however, well-ordered in a recently reported homologous rat ZP-C structure.
Such a flexible and temporarily-modulated association of the EHP segment with the ZP domain has been proposed to control the polymerization of ZP domain-containing proteins. Our findings suggest that this flexibility also extends to the ZP domain of TGFR-3 and might facilitate co-receptor ligand interaction and presentation via the adjacent FG-loop.
In all ZP structures solved to date, the EHP segment folds back onto the ZP-C subdomain via a flexible FG-loop
In case of the bridging residues 730 to 744 in the FG loop we observe residual, however non-interpretable, difference density hinting that this segment remained largely intact in the crystals and that the lack of defined electron density is caused by conformational disorder in this segment
Cross-references: PDB:4AJV
Protein: DP02636 (UniProt O88393)
Region: residues 730	to 744
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the murine 2.7 Å crystal structure that we are presenting here, the FG-loop is disordered, however, well-ordered in a recently reported homologous rat ZP-C structure.
Such a flexible and temporarily-modulated association of the EHP segment with the ZP domain has been proposed to control the polymerization of ZP domain-containing proteins. Our findings suggest that this flexibility also extends to the ZP domain of TGFR-3 and might facilitate co-receptor ligand interaction and presentation via the adjacent FG-loop.
In all ZP structures solved to date, the EHP segment folds back onto the ZP-C subdomain via a flexible FG-loop
In case of the bridging residues 730 to 744 in the FG loop we observe residual, however non-interpretable, difference density hinting that this segment remained largely intact in the crystals and that the lack of defined electron density is caused by conformational disorder in this segment
Cross-references: PDB:4AJV
Protein: DP02637 (UniProt P07237)
Region: residues 323	to 334
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The residues corresponding to the β5 strand and the following β5–α4 loop are absent from the electron density map due to disorder.
No electron density was observed for P135, E348–S357 (the x‐linker), the N‐terminal GPLGS cloning linker and, additionally, residues E323–L334 for chain A and E322–A336 for chain B that correspond to the strand β5 and β5–α4 loop in the b′x crystal structure.
The β5 strand, which normally forms β‐sheet with the β4 strand, is disordered in the dimeric structure.
Cross-references: PDB:4JU5
Protein: DP02637 (UniProt P07237)
Region: residues 348	to 357
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
PDI, also known as PDIA1, is the founding member and the most studied protein in the PDI family. PDI contains four thioredoxin‐like domains abb′a′, where a denotes catalytic domains containing CxxC motifs and b stands for non‐catalytic domains, with a 20‐residue x‐linker between b′ and a′ domain and a C‐terminal acidic tail.
The construct (residues 135–357) includes the bb′ domains and half of the x‐linker and yields high‐quality NMR spectra that were used to determine the NMR solution structure of the monomeric form
No electron density was observed for P135, E348–S357 (the x‐linker), the N‐terminal GPLGS cloning linker and, additionally, residues E323–L334 for chain A and E322–A336 for chain B that correspond to the strand β5 and β5–α4 loop in the b′x crystal structure.
Cross-references: PDB:4JU5