LiteFold/DisProt huggingface dataset:
Protein: DP03226 (UniProt P30771)
Region: residues 213	to 224
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the Upf1-RNA-ADP:AlF4 complex, there is no ordered electron density for the 13-residue linker that would connect the last residue of the CH domain (Thr212y) to the first residue of the stalk (Ile225y). The two ordered ends of the CH and helicase regions are located on the same side of the molecule at a distance of 30 A˚ from each other, which can be spanned by the disordered and flexible linker.
The linker with no ordered electron density consists of 12 residues.
Cross-references: PDB:2XZL
Protein: DP03226 (UniProt P30771)
Region: residues 213	to 224
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the Upf1-RNA-ADP:AlF4 complex, there is no ordered electron density for the 13-residue linker that would connect the last residue of the CH domain (Thr212y) to the first residue of the stalk (Ile225y). The two ordered ends of the CH and helicase regions are located on the same side of the molecule at a distance of 30 A˚ from each other, which can be spanned by the disordered and flexible linker.
The linker with no ordered electron density consists of 12 residues.
Cross-references: PDB:2XZL
Protein: DP03227 (UniProt P15205)
Region: residues 2212	to 2338
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Here we focus on the intrinsically disordered microtubule binding domain of the light chain of MAP1B.
The 1H–15N HSQC spectrum of the NH2 terminus of the light chain of MAP1B shows the for intrinsically disordered proteins typical narrow peak dispersion in the 1H dimension (Fig. 1).
Protein: DP03228 (UniProt P26447)
Region: residues 91	to 101
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model of Ca2+-bound S100A4 exhibits good stereochemistry and consists of 176 amino acids (dimer in the asymmetric unit), 51 water molecules and four calcium ions.
In S100A4, the C-terminal loop is long and very basic and makes it unique in comparison to other S100 proteins; however, in the Ca2+-bound S100A4 crystal structure the C-terminal loop (Phe89-Lys101) was disordered in the electron density maps.
Region 91-101 is disordered in the structure.
Cross-references: PDB:3CGA
Protein: DP03229 (UniProt P05451)
Region: residues 23	to 35
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 13 residues, including the O-glycosylation site, Thr5, are disordered in the crystal. Although the first N-terminal residue of our model (Cysl4) is well defined in electron density (Figure 1), no electron density is present for the adjacent N terminal residues.
Although at this temperature thermal disorder should be minimal, no density corresponding to the missing amino acids was observed. This indicates that residues 1-13 are statically disordered in the crystal.
HLIT and the C-type lectins differ at two levels: the extreme conformational flexibility of the N-terminal segment of HLIT (residues 1-13) and the lack of both calcium- and carbohydrate-binding sites.
The IDR characterized in the publication and spanning residues 1-13 corresponds to region 23-35 of the amino acid sequence, since the natural precursor form of the protein contains a signal peptide (1-22).
Cross-references: PDB:1LIT
Protein: DP03229 (UniProt P05451)
Region: residues 23	to 35
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal domain is a 13-residue peptide chain that stretches out of the heart shape of the C-type lectin domain. Three residues (positions 9–11) are involved in a helix turn motif that represented the only secondary element of this domain. As a result, the N-terminal domain was much more agitated in the crystal (averaged B-factor of 36 Å2) than the rest of the protein (averaged B-factor of 22 Å2).
The IDR characterized in the publication and spanning residues 1-13 corresponds to region 23-35 of the amino acid sequence, since the natural precursor form of the protein contains a signal peptide (1-22).
Cross-references: PDB:1QDD
Protein: DP03229 (UniProt P05451)
Region: residues 25	to 29
Annotation: glycosylation display site (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
During structure refinement, we observed a large electron density around Thr5, clearly indicating the presence of O-linked sugars to the Thr5 side chain.
The O-glycosylation site (Thr5) characterized in the publication corresponds to Thr27 in the amino acid sequence, since the natural precursor form of the protein contains a signal peptide (1-22).
Cross-references: PDB:1QDD
Protein: DP03229 (UniProt P05451)
Region: residues 24	to 33
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The CD spectrum (Fig. 2) was typical of a random coil structure (28) and strengthened our x-ray data. The negative band near 200 nm had an intensity in the range of those observed with model peptides with no steric constraints or internal hydrogen bonds. Random coil CD spectra were characterized by an intense negative band at 200 nm due to π-π* transition and low intensity bands near 210 nm due to n- π* transitions (28). No typical secondary structures could be deduced from this spectrum. Similar results were obtained in trifluoroethanol or SDS (data not shown). Both x-ray and CD experiments therefore suggest that pE1R11 is a highly flexible molecule that can display many configurations depending on the environment.
The authors also used a synthetic peptide which is almost identical to the first 11 residues (the 1. residue is different). The peptide sequence corresponds to region 23-33 of the amino acid sequence, since the natural precursor form of the protein contains a signal peptide (1-22).
Protein: DP03229 (UniProt P05451)
Region: residues 24	to 33
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: protein inhibition evidence used in manual assertion
Supporting statements:
The glycosylated aminoterminal undecapeptide generated by limited trypsin hydrolysis inhibited CaCO, crystal growth with a Kd = 3.0x10e6 mol/L, similar to that of lithostathine. On the contrary, the carboxy-terminal polypeptide was inactive. A synthetic undecapeptide identical to the N-terminal end but not glycosylated was equally active. The activity disappeared upon digestion of the undecapeptide with V8 protease. The N-terminal undecapeptide of lithostathine is therefore essential to the inhibitory activity of the protein on CaCO, crystal growth.
As shown on Figure 2A, the rate of disappearance of calcium from the solution containing seed crystals was decreased in the presence of lithostathine. The N-terminal undecapeptide of lithostathine and its synthetic analogue showed similar activity (Figures 2B and 3).
We studied in vitro the inhibitory properties of human lithostathine on CaCO, precipitation. The inhibitory activity was localized to the amino-terminal undecapeptide of the molecule.
On the contrary, the undecapeptide had retained the inhibitory properties of lithostathine, with a similar Kd for CaCO, crystals (3.0 x 10-6 mol/L). Abolition of inhibition after treating the peptide with protease V8, which generates three fragments, suggested that the glycan chain was not responsible by itself for the inhibition. Actually, it might not be involved at all, because a synthetic peptide with the sequence of the undecapeptide but without glycan was equally active, with a Kd of 4.1 X 10-6 mol/L (Figure 3B).
The authors used two undecapeptides (one of them was glycosylated), which are almost identical to the first 11 residues (the 1. residue is different) of the mature protein. The peptide sequence corresponds to region 23-33 of the amino acid sequence, since the natural precursor form of the protein contains a signal peptide (1-22).
Protein: DP03230 (UniProt P11940)
Region: residues 179	to 199
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structures were solved by molecular replacement using the RRM1-2·poly(A)11 crystal structure (PDB code 1cvj). The C-termini of both structures are disordered. The final model of the orthorhombic crystal form includes residues G99-S175. The final model of the trigonal crystal form includes residues G99-E178.
Overlay of the ternary complex with the free RRM2 domain shows the absence of the C-terminal helix α3 in the unliganded forms (Figure S3B). Residues 179 to 199 are disordered in both crystal forms in the absence of RNA but form an α-helix in the ternary complex.
Our NMR and crystallography studies (Figure S3) have suggested that the linkers connecting the RRM domains are flexible in the absence of RNA. As the result of this flexibility, the RRM domains are free to adopt different orientations.
Cross-references: PDB:4F25
PDB:4F26
Protein: DP03230 (UniProt P11940)
Region: residues 180	to 190
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final PABP RRM1/2–RNA model consists of 53 water molecules and 8 protein–nucleic acid complexes: complex A, PABP residues 11–179 plus nucleotides Ade-1 to Ade-8; complex B, PABP 11–132, 137–159, 170–175 plus Ade-3 to Ade-8; complex C, PABP 11–179 plus Ade-3 to Ade-8; complex D, PABP 11–132, 137–175 plus Ade-3 to Ade-8; complex E, PABP 11–179 plus Ade-2 to Ade-8; complex F, PABP 11–101, 112–132, 137–149, 168–173 plus Ade-3 to Ade-8; complex G, PABP 11–175 plus Ade-3 to Ade-8; complex H, PABP 11–103, 113–132, 137–152, 173–175 plus Ade-3 to Ade-8.
As suggested for the domain linker between RRM1 and RRM2, we believe that the RRM2/3 and RRM3/4 domain linkers are disordered in the absence of RNA.
Cross-references: PDB:1CVJ
Protein: DP03230 (UniProt P11940)
Region: residues 179	to 190
Annotation: flexible linker (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Our NMR and crystallography studies (Figure S3) have suggested that the linkers connecting the RRM domains are flexible in the absence of RNA. As the result of this flexibility, the RRM domains are free to adopt different orientations.
According to Figure 1, the RRM2/3 linker includes residues 176-190. Linker residues 179-190 are disordered in the structures (PDB: 4F25 and 4F26).
Cross-references: PDB:4F25
PDB:4F26
Protein: DP03230 (UniProt P11940)
Region: residues 179	to 183
Annotation: mRNA binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Helices following RRM1 (residues 92–96) and RRM2 (residues 176–183) contribute to RNA binding. R94 makes hydrogen bonds with the hydroxyl oxygen (O20) of the ribose moieties rA5 and rA6 while R179 forms hydrogen bonds with the phosphate oxygens of rA2.
In the α helices, key arginine residues, Arg94 in the first helix and Arg179 in the second, contribute to poly(A) binding by forming hydrogen bonds with the hydroxyl oxygen (O2) of the ribose moieties of rA5 and rA6 and the backbone phosphate oxygen of rA2 (Figures 3D and 3E). 
Linker residues 179-190 are disordered in the structures (PDB: 4F25 and 4F26) and residues 179-183 contribute to RNA binding (PDB: 4F02).
Cross-references: PDB:4F02
Protein: DP03230 (UniProt P11940)
Region: residues 179	to 190
Annotation: RNA binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
The importance of this second helix, which was not observed in the binary complex, was quantified by measuring the RNA binding affinity of a fragment (RRM1-2ΔR) that lacks the 13 C-terminal residues. ITC measurements revealed a 2.7-fold loss of affinity of RRM1-2ΔR (1.6 mM) relative to the larger crystallized fragment (Kd 0.6 mM; Figure S1B).
Linker residues 179-190 are disordered in the structures (PDB: 4F25 and 4F26).
Protein: DP03230 (UniProt P11940)
Region: residues 179	to 190
Annotation: disorder to order (Structural transition)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
Analysis of the scattering profiles using the program GNOM (Svergun, 1992) shows that the radius of gyration (Rg) of RRM1-2-3 is significantly larger for the poly(A)- bound form than without RNA (Table S2). The ab initio models of RRM1 2-3 generated by the software DAMMIF (Volkov and Svergun, 2003) show that the poly(A)-bound form of RRM1-2-3 in solution is more extended with a longer maximum dimension (Dmax) than the unbound RRM1-2-3 (Figures 5A and 5B and Table S2). Our NMR and crystallography studies (Figure S3) have suggested that the linkers connecting the RRM domains are flexible in the absence of RNA. As the result of this flexibility, the RRM domains are free to adopt different orientations. Our SAXS data show that this leads to a more compact conformation. In contrast, upon binding to poly(A), the linkers between the RRMs fold into a helices (Figure S3), leading to a more extended conformation (Figures 5A and 5B).
According to Figure 1, the RRM2/3 linker includes residues 176-190. Linker residues 179-190 are disordered in the structures (PDB: 4F25 and 4F26).
Protein: DP03230 (UniProt P11940)
Region: residues 1	to 10
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final PABP RRM1/2–RNA model consists of 53 water molecules and 8 protein–nucleic acid complexes: complex A, PABP residues 11–179 plus nucleotides Ade-1 to Ade-8; complex B, PABP 11–132, 137–159, 170–175 plus Ade-3 to Ade-8; complex C, PABP 11–179 plus Ade-3 to Ade-8; complex D, PABP 11–132, 137–175 plus Ade-3 to Ade-8; complex E, PABP 11–179 plus Ade-2 to Ade-8; complex F, PABP 11–101, 112–132, 137–149, 168–173 plus Ade-3 to Ade-8; complex G, PABP 11–175 plus Ade-3 to Ade-8; complex H, PABP 11–103, 113–132, 137–152, 173–175 plus Ade-3 to Ade-8.
Residues 1-10 are completely missing in all chains and are presumably disordered.
Cross-references: PDB:1CVJ
Protein: DP03231 (UniProt P15498)
Region: residues 130	to 141
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Dashed lines indicate regions not observed in the electron density map.
The current model contains two Vav1 CADPZ monomers (labeled A and B,respectively) in the asymmetric unit with backbone root-mean-square deviation (rmsd) of 0.13 A ̊for residues 2–129, 142–150, 156–180, 189–417,419–456, 463–478, 482–564.
Cross-references: PDB:3KY9
Protein: DP03231 (UniProt P15498)
Region: residues 565	to 584
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Dashed lines indicate regions not observed in the electron density map.
The current model contains two Vav1 CADPZ monomers (labeled A and B,respectively) in the asymmetric unit with backbone root-mean-square deviation (rmsd) of 0.13 A ̊for residues 2–129, 142–150, 156–180, 189–417,419–456, 463–478, 482–564.
Cross-references: PDB:3KY9
Protein: DP03232 (UniProt Q7KZF4)
Region: residues 660	to 669
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A long loop between SN4 and SN5 domains (residues 635–644) was disordered without visible electron density.
A loop between SN4 and SN5 (residues 635–644) is disordered and is displayed as a dotted line.
The aforementioned IDR corresponds to region 660-669 of the UniProt sequence.
Cross-references: PDB:3BDL
Protein: DP03232 (UniProt Q7KZF4)
Region: residues 660	to 669
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Tudor-SN contains four tandem repeats of staphylococcal nuclease-like domains (SN1-SN4) followed by a tudor and C-terminal SN domain (SN5).
A loop between SN4 and SN5 (residues 635–644) is disordered and is displayed as a dotted line.
A long loop between SN4 and SN5 domains (residues 635–644) was disordered without visible electron density.
The aforementioned IDR corresponds to region 660-669 of the UniProt sequence.
Cross-references: PDB:3BDL
Protein: DP03233 (UniProt Q92900-2)
Region: residues 219	to 228
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The conserved loop L9 (residues 219–224) is poorly ordered in all structures, although it is in the vicinity of the long linker connecting the two interacting regions of UPF2.
However, the first part of this linker (1130–1145) has certain conserved features and is partially visible in the electron density in the vicinity of residues 219–224 of UPF1 loop L9, suggesting that both these regions may be involved in additional interactions at some stage during complex assembly.
Residues 219–228 are disordered in the unbound structure and become partially ordered in the UPF2-bound form (PDB 2WJV). The sequence in the PDB corresponds to isoform 2 of protein UPF1.
Cross-references: PDB:2WJV
PDB:2WJY
Protein: DP03233 (UniProt Q92900-2)
Region: residues 219	to 228
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The conserved loop L9 (residues 219–224) is poorly ordered in all structures, although it is in the vicinity of the long linker connecting the two interacting regions of UPF2.
Residues 219–228 are not visible in the electron density map. The sequence in the PDB corresponds to isoform 2 of protein UPF1.
Cross-references: PDB:2WJY
Protein: DP03234 (UniProt P49915)
Region: residues 312	to 321
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 25–693 and 23–693 have been modeled for subunits A and B, respectively (Fig. 1a), with the exception of some flexible regions with no electron density in chain A (35–36, 79–85, 121–127, 312–321) and in chain B (123–125, 312–321).
Cross-references: PDB:2VXO
Protein: DP03235 (UniProt P50148)
Region: residues 1	to 216
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For Gαq, we were only able to build a model for residues 217–359 due to the weaker cryoEM map density in the N-terminal region compared to Gαi1.
The majority of the Ras-like domain residues of both Gαi1 (residues 32–54 and 193–354) and Gαq (residues 217–359) were also unambiguously modeled in these maps.
Cross-references: PDB:6VU5
Protein: DP03236 (UniProt Q9UDY8)
Region: residues 469	to 480
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As expected, the secondary structure elements are highly conserved between the two structures, and most of the changes occur in flexible loops connecting them (Fig. 2a, b, and d). Closer inspection of MALT1 and comparison with caspases reveal that the enzyme, albeit in its dimeric form and without the requirement of further processing to be active, has crystallized in an inactive state: loop L2 (residues 463–485), which carries the active-site cysteine C464 and forms the linker between the large and small subunits in caspases, appears flexible in MALT1 with residues 467–480 completely disordered in the electron density.
Binding of the covalent peptidic inhibitor induces the active conformation of MALT1. This transition involves structural changes especially in the loops L2, L3, and, to a lesser extent, L4, which delineate the active site but propagate throughout the molecule (Fig. 2a and d). Most prominently, loop L2, which is disordered in the inactive state of ligand-free MALT1, can be fully traced in the electron density of the inhibitor-bound structures.
PDB:3V55 and PDB:3V4O corresponds to the crystal structures of human MALT1(334-719) in its ligand free form and of of human MALT1 (caspase domain) in complex with an irreversible peptidic inhibitor, respectively.
Cross-references: PDB:3V55
Protein: DP03236 (UniProt Q9UDY8)
Region: residues 469	to 480
Annotation: small molecule binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Binding of the covalent peptidic inhibitor induces the active conformation of MALT1. This transition involves structural changes especially in the loops L2, L3, and, to a lesser extent, L4, which delineate the active site but propagate throughout the molecule (Fig. 2a and d). Most prominently, loop L2, which is disordered in the inactive state of ligand-free MALT1, can be fully traced in the electron density of the inhibitor-bound structures.
PDB:3V55 and PDB:3V4O corresponds to the crystal structures of human MALT1(334-719) in its ligand free form and of of human MALT1 (caspase domain) in complex with an irreversible peptidic inhibitor, respectively.
Cross-references: PDB:3V4O
Protein: DP03236 (UniProt Q9UDY8)
Region: residues 469	to 480
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Binding of the covalent peptidic inhibitor induces the active conformation of MALT1. This transition involves structural changes especially in the loops L2, L3, and, to a lesser extent, L4, which delineate the active site but propagate throughout the molecule (Fig. 2a and d). Most prominently, loop L2, which is disordered in the inactive state of ligand-free MALT1, can be fully traced in the electron density of the inhibitor-bound structures.
Cross-references: PDB:3V4O
Protein: DP03236 (UniProt Q9UDY8)
Region: residues 566	to 579
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The intervening loop between the paracaspase domain and Ig domain, which extends from strand β6 of the caspase-like fold to helix α1 of the Ig fold, is likely flexible in solution as it is partially disordered in the crystal structure (Fig. 1B).
The intervening peptide sequences between the paracaspase domain and the Ig fold are disordered and are represented here as gray dotted lines.
Cross-references: PDB:3UOA
PDB:3UO8
Protein: DP03236 (UniProt Q9UDY8)
Region: residues 566	to 579
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The intervening loop between the paracaspase domain and Ig domain, which extends from strand β6 of the caspase-like fold to helix α1 of the Ig fold, is likely flexible in solution as it is partially disordered in the crystal structure (Fig. 1B).
The intervening peptide sequences between the paracaspase domain and the Ig fold are disordered and are represented here as gray dotted lines.
Cross-references: PDB:3UOA
PDB:3UO8