LiteFold/DisProt huggingface dataset:
Protein: DP02803 (UniProt Q96Q11)
Region: residues 128	to 139
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The tail domain of hmtCCase (residues 355–405) as well as a stretch of 11 amino acid residues (99–110) within the head domain are completely disordered in the structure.
This IDR corresponds to the stretch of 11 amino acid residues, whose numbering in the publication is referred to the multiple sequence alignment of Figure 1.
Cross-references: PDB:1OU5
Protein: DP02803 (UniProt Q96Q11)
Region: residues 384	to 434
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The tail domain of hmtCCase (residues 355–405) as well as a stretch of 11 amino acid residues (99–110) within the head domain are completely disordered in the structure.
This IDR corresponds to the tail domain of hmtCCase, whose numbering in the publication is referred to the multiple sequence alignment of Figure 1.
Cross-references: PDB:1OU5
Protein: DP02804 (UniProt P61587)
Region: residues 1	to 19
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In RhoE, electron density is well defined for residues Gln20 to Lys200, whereas in ROCK-I residues 6–404 are similarly well resolved.
Cross-references: PDB:2V55
Protein: DP02804 (UniProt P61587)
Region: residues 1	to 19
Annotation: phosphorylation display site (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
ROCK-I phosphorylates the unconventional G-protein RhoE on multiple N- and C-terminal sites. These phosphorylation events stabilise RhoE, which functions to antagonise RhoA-induced stress fibre assembly.
Importantly, Ser7 and Ser11 of RhoE are sites of ROCK-I phosphorylation (Riento et al, 2005a).
Within the context of the crystal structure, the two ROCK-I phosphorylation sites present in RhoE (Ser7 and Ser11) are likely interchanging at the catalytic (primary binding) site, with resultant low substrate occupancy and consequently disordered and poorly resolved electron density.
Cross-references: PDB:2V55
Protein: DP02804 (UniProt P61587)
Region: residues 1	to 19
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The interaction of RhoE with ROCK-I positions RhoE to present both its N and C termini in close proximity to the kinase catalytic site cleft (Figure 5A). The visible N and C termini of RhoE (residues 20 and 200, respectively) are located some 20 Å from the kinase phosphoacceptor-binding site.
Model building studies, extending the polypeptide chain N-terminal from Gln20, and with reference to the position of the GSK3β peptide bound to PKBβ (Yang et al, 2002), indicate that both N-terminal phosphorylation sites, Ser7 and Ser11, are within reach of the catalytic site (Figure 5A).
Cross-references: PDB:2V55
Protein: DP02805 (UniProt Q91WA6)
Region: residues 301	to 341
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible linker connecting the UBL and NZF domains, as shown in Figure 3A
Cross-references: PDB:5Y3T
Protein: DP02805 (UniProt Q91WA6)
Region: residues 301	to 341
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Flexible linker connecting the UBL and NZF domains, as shown in Figure 3A
Cross-references: PDB:5Y3T
Protein: DP02806 (UniProt P0CY08)
Region: residues 103	to 132
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Cleavage of the purified al protein with chymotrypsin generates two major fragments...This analysis showed that the larger fragment consists of amino acids 1-102 and the smaller fragment consists of amino acids 132-210 of al (210 residues total).
The limited proteolysis experiments identify residues 103-131 as the flexible linker
Protein: DP02806 (UniProt P0CY08)
Region: residues 113	to 132
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The otherwise flexible amino-terminal extension of the MATalpha2 homeodomain forms a beta-hairpin that grips the MCM1 surface through parallel beta-strand hydrogen bonds and close-packed, predominantly hydrophobic, side chains.....An unusual feature of the complex is that an eight-amino-acid sequence adopts an alpha-helical conformation in one of two copies of the MATalpha2 monomer and a beta-strand conformation in the other. This 'chameleon' sequence of MATalpha2 may be important for recognizing natural operator sites.
The structure shows that α2 uses a short eight-amino-acid module in the linker region to bind MCM1 via parallel β-strands. This recognition strand is tethered to the α2 homeodomain by a segment of unusual conformational flexibility. 
The cis copy of the α2 flexible linker implicated in the interaction with MCM1 (refs 23,26) forms a β-hairpin with a type-I turn.
The results compared to the flexible region identified by proteolysis, indicate that residues 113-132 become ordered upon binding MCM1 and DNA. This structure consists of a beta strand (113-120) involved in MCM1 binding, plus a "chameleon" region (121-128) that can be either a beta strand or a helix
The α2 residues 121–128, QDMINKST, have the unusual property of forming either an α-helix or a β-strand. 
Cross-references: PDB:1MNM
Protein: DP02806 (UniProt P0CY08)
Region: residues 103	to 132
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The α2 residues 121–128, QDMINKST, have the unusual property of forming either an α-helix or a β-strand. 
This paper demonstrates the two domains are joined by a flexible linker
Protein: DP02806 (UniProt P0CY08)
Region: residues 110	to 128
Annotation: protein binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
An a2 fragment beginning with residue 120 retains partial cooperative binding with MCMl , and a fragment that starts with residue 128 fails to show strong cooperative binding with MCMl. These results suggest that approximately 20 residues (110-l 28) adjacent to the homeodomain are required for cooperative binding with MCMl. 
This paper demonstrates the linker region is required for cooperative MCM1 binding
Protein: DP02806 (UniProt P0CY08)
Region: residues 110	to 128
Annotation: molecular function regulator (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
An a2 fragment beginning with residue 120 retains partial cooperative binding with MCMl , and a fragment that starts with residue 128 fails to show strong cooperative binding with MCMl. These results suggest that approximately 20 residues (110-l 28) adjacent to the homeodomain are required for cooperative binding with MCMl. 
This paper demonstrates the linker region is required for cooperative MCM1 binding, it is a protein protein interaction that regulates DNA operator recognition
Protein: DP02806 (UniProt P0CY08)
Region: residues 114	to 121
Annotation: molecular function regulator (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The structure shows that α2 uses a short eight-amino-acid module in the linker region to bind MCM1 via parallel β-strands. 
The otherwise flexible amino-terminal extension of the MATalpha2 homeodomain forms a beta-hairpin that grips the MCM1 surface through parallel beta-strand hydrogen bonds and close-packed, predominantly hydrophobic, side chains
With the exception of Val 119, each of the α2 residues between Leu 114 and Gln 121 (LVFNVVTQ) makes van der Waals contacts with MCM1 residues.
Protein: DP02806 (UniProt P0CY08)
Region: residues 190	to 210
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The a2 fragment used in our crystallographic study extends to the C-terminal end of a2 and therefore contains an additional 22 residues following the C-terminus of the homeodomain. This C-terminal tail may mediate the interaction between a2 and al (A. Mak and A. D. J., unpublished data; see also Strathern et al., 1988). We do not see clear electron density for this region and presume that it is disordered in the crystal. 
The region actually corresponds to 21 residues 190-210 as shown by the crystal structure
Cross-references: PDB:1APL
Protein: DP02806 (UniProt P0CY08)
Region: residues 193	to 203
Annotation: molecular function regulator (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We found that the a1 homeodomain perturbs the resonances of only the C-terminal tail of a2; moreover, contact with a1 converts a portion of this tail (residues 193-203) from its unstructured state to an a-helix, as determined by J coupling and NOE measurements
These NOE cross peak volume data suggest that residues 194-200 are helical. 
Binding to MAT alpha 1 structures the C terminal tail into a helix as shown by NMR
Protein: DP02806 (UniProt P0CY08)
Region: residues 193	to 203
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
We found that the a1 homeodomain perturbs the resonances of only the C-terminal tail of a2; moreover, contact with a1 converts a portion of this tail (residues 193-203) from its unstructured state to an a-helix, as determined by J coupling and NOE measurements
These NOE cross peak volume data suggest that residues 194-200 are helical. 
Binding to MAT alpha 1 structures the C terminal tail into a helix as shown by NMR
Protein: DP02806 (UniProt P0CY08)
Region: residues 190	to 205
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The a1 and a2 homeodomains bind in a head-to-tail orientation, with heterodimer contacts mediated by a 16-residue tail located carboxyl-terminal to the a2 homeodomain. This tail becomes ordered in the presence of al, part of it forming a short amphipathic helix that packs against the a1 horneodomain between helices 1 and 2
The a2 protein contacts the a1 homeodomain with a peptide tail located COOHterminal to the a2 homeodomain. As compared with the structure of a2 alone bound to DNA, an additional 16 residues are ordered in the ternary complex. This COOHterminal tail, consisting of residues 59 to 74
Numbering is shifted by 131 residues according to UNIPROT accession, and the region corresponds to residues 190-205 of the UNIPROT sequence
Cross-references: PDB:1YRN
Protein: DP02806 (UniProt P0CY08)
Region: residues 190	to 205
Annotation: molecular function regulator (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The a1 and a2 homeodomains bind in a head-to-tail orientation, with heterodimer contacts mediated by a 16-residue tail located carboxyl-terminal to the a2 homeodomain. This tail becomes ordered in the presence of al, part of it forming a short amphipathic helix that packs against the a1 horneodomain between helices 1 and 2
The a2 protein contacts the a1 homeodomain with a peptide tail located COOHterminal to the a2 homeodomain. As compared with the structure of a2 alone bound to DNA, an additional 16 residues are ordered in the ternary complex. This COOHterminal tail, consisting of residues 59 to 74
Numbering is shifted by 131 residues according to UNIPROT accession, and the region corresponds to residues 190-205 of the UNIPROT sequence. Function of this region is binding to MAT 1 alpha
Cross-references: PDB:1YRN
Protein: DP02808 (UniProt P53927)
Region: residues 179	to 191
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Figure 1. Helices α4 and αC are not visible in the Nop15 crystal structure (chain A) and are drawn with dotted lines
The missing residues in the crystal structure correspond to residues 179-191
Cross-references: PDB:5T9P
Protein: DP02808 (UniProt P53927)
Region: residues 181	to 220
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR: The average intensity of the C-terminal resonances was 4 times higher than those of the central RRM domain (P < 0.0001). Therefore, our NMR results indicate that the C-terminal region tumbles as a flexible moiety at a rate faster than the core RRM domain (Figure (Figure4D4D).
The flexible residues from NMR analysis correspond to residues 181-220
Small-angle X-ray scattering, NMR and RNA-binding analyses further reveal that the C-terminal residues of Nop15 are highly flexible
Protein: DP02808 (UniProt P53927)
Region: residues 181	to 220
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
SAXS: we used SAXS to study Nop1581–220 (Figure (Figure4A,4A, Supplementary Table S3). We evaluated the SAXS data using the EOM, which allows fitting of an ensemble of structures for flexible protein regions. The selected set of three conformers that optimally fit the SAXS data indicated that the C-terminal residues (181–220) are highly flexible, widely sampling around the core RRM domain (Figure (Figure4A4A and B).
The flexible residues from SAXS analysis correspond to residues 181-220
Small-angle X-ray scattering, NMR and RNA-binding analyses further reveal that the C-terminal residues of Nop15 are highly flexible
Protein: DP02808 (UniProt P53927)
Region: residues 181	to 220
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Small-angle X-ray scattering, NMR and RNA-binding analyses further reveal that the C-terminal residues of Nop15 are highly flexible, but essential for tight RNA binding. Moreover, comparison with a recently reported cryo-electron microscopy structure indicates that dramatic rearrangement of the C-terminal region of Nop15 in the pre-ribosome exposes the RNA-binding surface to recognize the base of its stem-loop target RNA
Comparing our crystal structure with Nop15 in a cryo-EM model of the pre-60S ribosome (17) indicates that the α-helical region is dramatically refolded, which releases the classical RNA-binding residues for interaction at the base of an ITS2 stem-loop and allows interaction of the C-terminal residues near the distal loop of the stem-loop.
The disorder to order transition is deduced from the comparison of the results of this paper with those of CryoEM structures where the same region is folded
Protein: DP02808 (UniProt P53927)
Region: residues 181	to 220
Annotation: disorder to order (Structural transition)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The disorder to order transition is deduced from the comparison of the results of this paper (region folded) with those of Crystal structures where the same region is unfolded or flexible

However, states A–C already contain a hallmark structure typically seen on Arx1 or Nog2 particles, termed the “foot,” which is formed by ITS2 rRNA and its associated “A3” cluster factors Cic1/Nsa3, Nop7, Nop15, and Rlp7

Cross-references: PDB:3JCT
Protein: DP02808 (UniProt P53927)
Region: residues 1	to 87
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There is no statement in the paper but residues 1-87 are disordered 
Cross-references: PDB:3JCT
Protein: DP02808 (UniProt P53927)
Region: residues 181	to 220
Annotation: molecular function regulator (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
Small-angle X-ray scattering, NMR and RNA-binding analyses further reveal that the C-terminal residues of Nop15 are highly flexible, but essential for tight RNA binding. Moreover, comparison with a recently reported cryo-electron microscopy structure indicates that dramatic rearrangement of the C-terminal region of Nop15 in the pre-ribosome exposes the RNA-binding surface to recognize the base of its stem-loop target RNA
Comparing our crystal structure with Nop15 in a cryo-EM model of the pre-60S ribosome (17) indicates that the α-helical region is dramatically refolded, which releases the classical RNA-binding residues for interaction at the base of an ITS2 stem-loop and allows interaction of the C-terminal residues near the distal loop of the stem-loop.
Our binding assays indicate that the residues of Nop15 C-terminal to the α3/α4 helices (181–220) are important for RNA binding
Moreover, removal of an additional 12 residues from the C-terminus (Nop1581–180) further weakened RNA-binding affinity to 30-fold weaker than Nop15 81–220. Together these results indicate that the C-terminal residues are paradoxically important for RNA recognition, despite sequestering the classical RNA-binding residues.
Protein: DP02808 (UniProt P53927)
Region: residues 181	to 220
Annotation: RNA binding (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
Small-angle X-ray scattering, NMR and RNA-binding analyses further reveal that the C-terminal residues of Nop15 are highly flexible, but essential for tight RNA binding. Moreover, comparison with a recently reported cryo-electron microscopy structure indicates that dramatic rearrangement of the C-terminal region of Nop15 in the pre-ribosome exposes the RNA-binding surface to recognize the base of its stem-loop target RNA
Comparing our crystal structure with Nop15 in a cryo-EM model of the pre-60S ribosome (17) indicates that the α-helical region is dramatically refolded, which releases the classical RNA-binding residues for interaction at the base of an ITS2 stem-loop and allows interaction of the C-terminal residues near the distal loop of the stem-loop.
Our binding assays indicate that the residues of Nop15 C-terminal to the α3/α4 helices (181–220) are important for RNA binding
Moreover, removal of an additional 12 residues from the C-terminus (Nop1581–180) further weakened RNA-binding affinity to 30-fold weaker than Nop15 81–220. Together these results indicate that the C-terminal residues are paradoxically important for RNA recognition, despite sequestering the classical RNA-binding residues.
Protein: DP02808 (UniProt P53927)
Region: residues 1	to 80
Annotation: RNA binding (Molecular function)
Evidence: experimental evidence used in manual assertion
Supporting statements:
Deletion of the N-terminal region that was not included in our crystal structure (residues 1–80) increased RNA-binding affinity 8 fold (Kd = 35.4 nM for Nop1581–220) (Figure ​(Figure2C2C and D, Table ​Table1).1).
Protein: DP02809 (UniProt P53193)
Region: residues 47	to 60
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The best results were obtained for variant Jac1-C2 (residues 5–182). Similar to Jac1-C1, Jac1-C2 crystallized with two molecules (A and B) in the asymmetric unit and diffracted X-rays to 1.85 Å resolution. The structure was determined for residues 8–181 (A) and 12–176 (B), but segments consisting of residues 47–60 and 95–98 (B) were not resolved.
Cross-references: PDB:3UO3
PDB:3UO2
Protein: DP02809 (UniProt P53193)
Region: residues 91	to 100
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of Jac1 is L-shaped and consists of 2 distinct α-helical domains (Fig. 1); the N-terminal J-domain (residues 11–84) and the C-terminal Isu binding C-domain (residues 101–184). These two domains are connected by a flexible linker (residues 85–100). 
Interestingly, the linker helix is ordered in molecule A of both Jac1 structures and disordered in molecule B, suggesting intrinsic flexibility of this region.
Cross-references: PDB:3UO2
Protein: DP02809 (UniProt P53193)
Region: residues 91	to 100
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The structure of Jac1 is L-shaped and consists of 2 distinct α-helical domains (Fig. 1); the N-terminal J-domain (residues 11–84) and the C-terminal Isu binding C-domain (residues 101–184). These two domains are connected by a flexible linker (residues 85–100). 
Interestingly, the linker helix is ordered in molecule A of both Jac1 structures and disordered in molecule B, suggesting intrinsic flexibility of this region.
Cross-references: PDB:3UO2
Protein: DP02810 (UniProt P02469)
Region: residues 494	to 540
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The partial LEa domain at the C-terminus is disordered and the structure is therefore referred to as β1 LN-LEa1–4 in this report.
Cross-references: PDB:4AQS
Protein: DP02811 (UniProt Q8K419)
Region: residues 2	to 12
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final crystallographic model consisted of 140 protein residues (corresponding to residues 12–164 of the mGal sequence deposited in GenBank as AAC27245.1), one lactose molecule, two glycerol molecules, part of a polyethylene glycol molecule (comprising two ethylene glycol units), one sodium cation and 189 water molecules.
Cross-references: PDB:3I8T
Protein: DP02812 (UniProt A6NI73)
Region: residues 147	to 157
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1 and 2, 106-116, and 136-138 were disordered. 91.8% of total residues were in the most favored regions, and 0% were in the disallowed regions of the Ramachandran plot.
The AB (residues 106-116) and CC′ (residues 136-138) loops of D2 were disordered (Fig. 1, A and C).
However, residues 106-116 of D2, which corresponds to the A′ strand of D1 in the other LRC receptors, was disordered.
Disordered residue 106-116 of the crystal structure corresponds to sequence residues 147-157
Cross-references: PDB:2D3V
Protein: DP02812 (UniProt A6NI73)
Region: residues 147	to 157
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The average B-factor of D2 (46.0 Å2) was higher than that of domain 1 (D1) (24.3 Å2), which may be due to the relatively loose packing of D2 in the crystal.
Disordered residue 106-116 of the crystal structure corresponds to sequence residues 147-157
Cross-references: PDB:2D3V