LiteFold/DisProt huggingface dataset:
Protein: DP01990 (UniProt P36894)
Region: residues 104	to 120
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The significance of the
rearrangement of the 45 loop is illustrated by the shifts of Phe85
and Gln86 of BMPR-IA into binding-competent positions. Gln86
represents the main binding determinant in the BMP-2-BMPRIA
interaction, demonstrating that a stable complex can be formed
only if the 45 loop adopts a helical structure.
Protein: DP01993 (UniProt Q80VP1)
Region: residues 229	to 407
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Circular dichroism (CD) spectra of the epsin DPW region show little absorption above 210 nm and a large minimum at 200 nm, indicating little secondary structure in solution
Protein: DP01993 (UniProt Q80VP1)
Region: residues 229	to 407
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Solution studies of the 17.7 kDa epsin DPW region (aa 229–407) indicate that the repeated binding motifs are highly accessible for interaction with the α-ear.
Protein: DP01993 (UniProt Q80VP1)
Region: residues 229	to 407
Annotation: disorder (Structural state)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Dynamic light scattering of the DPW region corroborates that this region is predominantly disordered in solution.
Protein: DP01993 (UniProt Q80VP1)
Region: residues 229	to 407
Annotation: protein binding (Molecular function)
Evidence: dynamic light scattering assay evidence used in manual assertion
Supporting statements:
Solution studies of the 17.7 kDa epsin DPW region (aa 229–407) indicate that the repeated binding motifs are highly accessible for interaction with the α-ear.
Protein: DP01994 (UniProt P27321)
Region: residues 629	to 652
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Gaps in the electron density of CAST4 are indicated by missing residues between D589 and K594, and between N629 and P652.
Cross-references: PDB:3bow
Protein: DP01994 (UniProt P27321)
Region: residues 187	to 285
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Intrinsic disorder in the free state enables calpastatin to structurally adapt upon binding to the substrate binding cleft of calpain, distantly resembling the inhibitory conformation of the broad-specificity, structured protease inhibitors, the cystatins15 (Suppl. Fig. 4).
Numbering in the publication correspond to this boundaries of the Uniprot sequence.
Protein: DP01994 (UniProt P27321)
Region: residues 194	to 205
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The divergent intervening sequences connecting regions A, B and C are devoid of electron density (red dots in Fig. 1a). NMR analysis of the complex between 15N-labeled calpastatin and unlabeled calpain (Fig. 1c, Suppl. Fig. 1a) corroborated the disorder in the calpastatin intervening sequences (orange in Fig. 1d), which were detectable and could be partially assigned. Conversely, calpastatin regions A, B and C bind calpain, become ordered and tumble slowly in solution as part of the 111 kDa complex, and were undetectable by NMR.
Cross-references: PDB:3DF0
Protein: DP01994 (UniProt P27321)
Region: residues 219	to 251
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The divergent intervening sequences connecting regions A, B and C are devoid of electron density (red dots in Fig. 1a). NMR analysis of the complex between 15N-labeled calpastatin and unlabeled calpain (Fig. 1c, Suppl. Fig. 1a) corroborated the disorder in the calpastatin intervening sequences (orange in Fig. 1d), which were detectable and could be partially assigned. Conversely, calpastatin regions A, B and C bind calpain, become ordered and tumble slowly in solution as part of the 111 kDa complex, and were undetectable by NMR.
Cross-references: PDB:3DF0
Protein: DP01994 (UniProt P27321)
Region: residues 268	to 278
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The divergent intervening sequences connecting regions A, B and C are devoid of electron density (red dots in Fig. 1a). NMR analysis of the complex between 15N-labeled calpastatin and unlabeled calpain (Fig. 1c, Suppl. Fig. 1a) corroborated the disorder in the calpastatin intervening sequences (orange in Fig. 1d), which were detectable and could be partially assigned. Conversely, calpastatin regions A, B and C bind calpain, become ordered and tumble slowly in solution as part of the 111 kDa complex, and were undetectable by NMR.
Cross-references: PDB:3DF0
Protein: DP01996 (UniProt Q07009)
Region: residues 245	to 260
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model (refined against data collected previously at the Cornell High Energy Synchrotron Source on P1 native crystal form) is well defined with the exception of the following disordered regions that were omitted: 245-260, 273-278, 292-321, 437-459 and 565-566 (indicated by dotted lines in Figure 1B).
Cross-references: PDB:1df0
Protein: DP01996 (UniProt Q07009)
Region: residues 292	to 321
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model (refined against data collected previously at the Cornell High Energy Synchrotron Source on P1 native crystal form) is well defined with the exception of the following disordered regions that were omitted: 245-260, 273-278, 292-321, 437-459 and 565-566 (indicated by dotted lines in Figure 1B).
Cross-references: PDB:1df0
Protein: DP01996 (UniProt Q07009)
Region: residues 437	to 459
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model (refined against data collected previously at the Cornell High Energy Synchrotron Source on P1 native crystal form) is well defined with the exception of the following disordered regions that were omitted: 245-260, 273-278, 292-321, 437-459 and 565-566 (indicated by dotted lines in Figure 1B).
Cross-references: PDB:1df0
Protein: DP01996 (UniProt Q07009)
Region: residues 527	to 536
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In domain IV, there are several disordered regions including residues 541-549 and residues 588-593 corresponding to EF hands 1 and 2, as well as the linker between domains III and IV, residues 527-536.
Cross-references: PDB:1qxp
Protein: DP01996 (UniProt Q07009)
Region: residues 527	to 536
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In domain IV, there are several disordered regions including residues 541-549 and residues 588-593 corresponding to EF hands 1 and 2, as well as the linker between domains III and IV, residues 527-536.
Protein: DP01999 (UniProt Q8K4J6)
Region: residues 67	to 98
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
circular dichroism (CD) experiments revealed that each RPEL peptide is largely unstructured in solution (α-helical content of 5.2, 4 and 4.3%, respectively) (Supplementary Figure S1), indicating that the observed RPEL peptide secondary structure is induced on binding actin.
Protein: DP01999 (UniProt Q8K4J6)
Region: residues 67	to 98
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
G-actin binds individual RPEL peptides from the MAL N-terminal regulatory domain
Protein: DP01999 (UniProt Q8K4J6)
Region: residues 67	to 98
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
circular dichroism (CD) experiments revealed that each RPEL peptide is largely unstructured in solution (α-helical content of 5.2, 4 and 4.3%, respectively) (Supplementary Figure S1), indicating that the observed RPEL peptide secondary structure is induced on binding actin.
G-actin binds individual RPEL peptides from the MAL N-terminal regulatory domain and the structural fold adopted by an RPEL motif
Protein: DP01999 (UniProt Q8K4J6)
Region: residues 111	to 142
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
circular dichroism (CD) experiments revealed that each RPEL peptide is largely unstructured in solution (α-helical content of 5.2, 4 and 4.3%, respectively) (Supplementary Figure S1), indicating that the observed RPEL peptide secondary structure is induced on binding actin.
Protein: DP01999 (UniProt Q8K4J6)
Region: residues 111	to 142
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
G-actin binds individual RPEL peptides from the MAL N-terminal regulatory domain
Protein: DP01999 (UniProt Q8K4J6)
Region: residues 111	to 142
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
circular dichroism (CD) experiments revealed that each RPEL peptide is largely unstructured in solution (α-helical content of 5.2, 4 and 4.3%, respectively) (Supplementary Figure S1), indicating that the observed RPEL peptide secondary structure is induced on binding actin.
G-actin binds individual RPEL peptides from the MAL N-terminal regulatory domain and the structural fold adopted by an RPEL motif
Protein: DP01999 (UniProt Q8K4J6)
Region: residues 155	to 186
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
circular dichroism (CD) experiments revealed that each RPEL peptide is largely unstructured in solution (α-helical content of 5.2, 4 and 4.3%, respectively) (Supplementary Figure S1), indicating that the observed RPEL peptide secondary structure is induced on binding actin.
Protein: DP01999 (UniProt Q8K4J6)
Region: residues 155	to 186
Annotation: protein binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
G-actin binds individual RPEL peptides from the MAL N-terminal regulatory domain
Protein: DP01999 (UniProt Q8K4J6)
Region: residues 155	to 186
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
circular dichroism (CD) experiments revealed that each RPEL peptide is largely unstructured in solution (α-helical content of 5.2, 4 and 4.3%, respectively) (Supplementary Figure S1), indicating that the observed RPEL peptide secondary structure is induced on binding actin.
G-actin binds individual RPEL peptides from the MAL N-terminal regulatory domain and the structural fold adopted by an RPEL motif
Protein: DP02000 (UniProt O14745)
Region: residues 242	to 358
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
This disordered state is supported by CD results of the isolated domains, which show that the PDZ2 domains are structured, but the CT domain is largely disordered.
Protein: DP02000 (UniProt O14745)
Region: residues 242	to 358
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The far-ultraviolet irradiation circular dichroism (CD) spectrum
of the isolated CT (Figure 3B) exhibits a strong negative band at 205 nm and a weak shoulder near 220 nm, consistent with a largely disordered conformation with little regular secondary structure
Protein: DP02000 (UniProt O14745)
Region: residues 242	to 358
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The spectra of  PDZ2-CT construct (residues 150–358) show a pronounced negative band at 222 nm indicative of helical conformation
Protein: DP02000 (UniProt O14745)
Region: residues 242	to 358
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The remaining unassigned peaks due to the C-terminal segment form a dense cluster in the center of the HSQC spectrum characteristic of a disordered conformation.
Cross-references: PDB:2JXO
Protein: DP02000 (UniProt O14745)
Region: residues 242	to 358
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The NMR results indicate that the last 11 residues at the C terminus of NHERF1 participate in binding and adopt an a-helical conformation when bound to PDZ2.
Protein: DP02000 (UniProt O14745)
Region: residues 242	to 358
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
the noncovalent complex between the isolated PDZ2 and CT domains serves as a reliable model for understanding the intramolecular interaction between PDZ2 and the C-terminal domain of NHERF1
Protein: DP02000 (UniProt O14745)
Region: residues 242	to 358
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15 N HSQC spectrum of PDZ2CT (amino acid residues 150–358) is characteristic of a heterogeneous conformation of a structured PDZ domain, coexisting with a largely disordered C-terminal region that typically yields a high density of sharp peaks between 8 and 8.5 ppm in the proton dimension.
Cross-references: PDB:2KRG
Protein: DP02001 (UniProt O08807)
Region: residues 256	to 274
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We modeled amino acid residues 79–241 and 247–255, but not those of the C-terminal segments, due to the lack of electron density (supplementary Fig. S5D, left).
Cross-references: PDB:3VWU
Protein: DP02001 (UniProt O08807)
Region: residues 244	to 263
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
They determined the crystal structure of P5 in complex with the Prdx4 C-terminal peptide (residues 244-263 from Mus musculus Prdx4). 
"peptide electron density was visible only for the region from Glu246 to Gly251, and, thus, we found it bound a hydrophobic groove of P5"
Cross-references: PDB:3W8J
Protein: DP02001 (UniProt O08807)
Region: residues 244	to 263
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
"Here, we established the structural basis of the interaction between Prx4 and PDIs by showing that a locally unstructured C-terminal segment of oxidized Prx4 binds to the peptide-binding groove of Trx"
Protein: DP02001 (UniProt O08807)
Region: residues 252	to 263
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
They determined the crystal structure of P5 in complex with the Prdx4 C-terminal peptide (residues 244-263 from Mus musculus Prdx4). "peptide electron density was visible only for the region from Glu246 to Gly251, and, thus, we found it bound a hydrophobic groove of P5
Cross-references: PDB:3W8J
Protein: DP02001 (UniProt O08807)
Region: residues 246	to 251
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
They determined the crystal structure of P5 in complex with the Prdx4 C-terminal peptide (residues 244-263 from Mus musculus Prdx4). "peptide electron density was visible only for the region from Glu246 to Gly251, and, thus, we found it bound a hydrophobic groove of P5
Cross-references: PDB:3W8J
Protein: DP02002 (UniProt O15922)
Region: residues 1	to 89
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There is no density for 89 residues at the N terminus, which were either not present or not ordered in those crystals.
Cross-references: PDB:2J63
Protein: DP02002 (UniProt O15922)
Region: residues 230	to 240
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Three additional disordered loops lie on the outer surface of the protein away from the active site.
Cross-references: PDB:2J63
Protein: DP02002 (UniProt O15922)
Region: residues 315	to 324
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Three additional disordered loops lie on the outer surface of the protein away from the active site.
Cross-references: PDB:2J63
Protein: DP02003 (UniProt P16220)
Region: residues 101	to 160
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Biochemical studies of intact CREB have demontrated that the pKID domain is unusually susceptible to proteolysis  [PMID:1671708] and hence likely to be unstructured. Biophysical characterization of the isolated pKID domain (residues 101 - 160 of human CREB, 60 residues) was limited in the original study of a pKID-CBP complex by the phosphopeptide’s sparing solubility in the absence of guanidine hydrochloride.
Protein: DP02003 (UniProt P16220)
Region: residues 101	to 160
Annotation: disorder to order (Structural transition)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
The three-dimensional structure of a CREB pKID-CBP regulatory complex has recently been described [PMID:9413984] and provides a model of a coil to helix transition on assembly of a transcriptional activator-coactivator complex.
Protein: DP02004 (UniProt Q92793)
Region: residues 674	to 1080
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In far-ultraviolet (UV) circular dichroism, ID3 has a strong negative peak around 200 nm, typical of random coil proteins, with a slight tendency to local secondary structure formation
Protein: DP02004 (UniProt Q92793)
Region: residues 999	to 1050
Annotation: protein binding (Molecular function)
Evidence: site-directed spin-labelling electron paramagnetic resonance evidence used in manual assertion
Supporting statements:
The PREs observed with the three ZFP106-f constructs confirmed the interaction and highlighted two significantly affected ID3 regions, one in the N-terminal region (NTR, 674–780) and the other in the C-terminal region (CTR, 999–1050) (Fig. 6b).
Further corroboration came with additional control experiments, in which the paramagnetic label free in solution (upon reduction of the disulfide bond between ZFP106-M2-cys and the label) also gave rise to same type of nonspecific signal in NTR of ID3, whereas it did not affect the signal at the CTR, confirming that the observed effects at the CTR of ID3 are due to the specific interaction of the two proteins (Supplementary Fig. S7d).
Protein: DP02004 (UniProt Q92793)
Region: residues 1852	to 2057
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The 1H-15N correlation spectrum exhibits all of the peculiar NMR features of an IDP, namely, a reduced chemical-shift dispersion that is particularly pronounced in the 1H dimension, and a high degree of signal crowding.
Protein: DP02004 (UniProt Q92793)
Region: residues 674	to 1080
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Both in SDS-PAGE and size-exclusion chromatography (SEC), the apparent molecular weight (Mw) of ID3 is about 70 kDa, two times its actual Mw, which is often the first indication of structural disorder16.
Protein: DP02004 (UniProt Q92793)
Region: residues 674	to 1080
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Both in SDS-PAGE and size-exclusion chromatography (SEC), the apparent molecular weight (Mw) of ID3 is about 70 kDa, two times its actual Mw, which is often the first indication of structural disorder
Protein: DP02004 (UniProt Q92793)
Region: residues 674	to 1080
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
SAXS, circular dichroism and NMR spectroscopy showed for ID3 a random coil state. By integrating 1H-detected and 13C-detected high-resolution multi-dimensional NMR experiments18, 20–22 we assigned about 95% of backbone chemical shifts, providing atomic resolution information on its structural and dynamic features.
Protein: DP02004 (UniProt Q92793)
Region: residues 674	to 1080
Annotation: disorder (Structural state)
Evidence: small-angle X-ray scattering evidence used in manual assertion
Supporting statements:
SAXS measurements [following removal of potential aggregates by high-pressure liquid chromatography (HPLC)] yielded an average radius of gyration (Rg) of 80 Å of the different conformers in solution (Fig. 1c and e), corresponding to a disordered state.
Protein: DP02004 (UniProt Q92793)
Region: residues 674	to 1080
Annotation: flexible linker (Disorder function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
In far-ultraviolet (UV) circular dichroism, ID3 has a strong negative peak around 200 nm, typical of random coil proteins, with a slight tendency to local secondary structure formation16 (Supplementary Fig. S1b)
The intrinsically disordered region 3 (ID3, aa674–1080) is located between the KIX domain and bromodomain of CBP.
Linking functions: an additional role for an intrinsically disordered linker domain in the transcriptional coactivator CBP.
Protein: DP02004 (UniProt Q92793)
Region: residues 674	to 1080
Annotation: protein binding (Molecular function)
Evidence: competitive binding evidence used in manual assertion
Supporting statements:
The free ID3 was found to compete with the ID3 of full-length CBP for binding the substrate, ZFP106-f, causing a significant concentration-dependent decrease in the acetylation of ZFP106-f (Fig. 4a).
Overall, these results show that ID3 specifically binds to ZFP106-f via defined sequence features.