LiteFold/DisProt huggingface dataset:
Protein: DP02858 (UniProt P18206-2)
Region: residues 857	to 867
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In this study, we first determined the solution structure of the tandem SH3 domains of CAP and further analyzed its complex structure with the proline-rich linker of vinculin using ITC, NMR, and X-ray crystallography.
The binding motif of the SH3 domain of Vinculin (857-879) is composed of two short proline-rich regions (prr): prr1 (N- LAPPKPPLPE -C), corresponding to PDB:4ln2, and prr2 (N- VPPPRPPPPE -C), corresponding to PDB:4lnp.
Cross-references: PDB:4ln2
Protein: DP02858 (UniProt P18206-2)
Region: residues 857	to 879
Annotation: molecular adaptor activity (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In this study, we first determined the solution structure of the tandem SH3 domains of CAP and further analyzed its complex structure with the proline-rich linker of vinculin using ITC, NMR, and X-ray crystallography.
Because no inter-domain NOEs are observed between the SH3a and SH3b domains after their binding to vin857 (data not shown), the enhanced binding affinity is most likely caused by the flexible linker, which tethers both the SH3a and SH3b domains and restricts the dissociation ability of the individual SH3 domains from the substrate.
Protein: DP02860 (UniProt P55211)
Region: residues 289	to 334
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final refined atomic model contains residues 140–288 and 335–416 for chains A and C, and 140–289 and 337–416 for chains B and D, respectively.
Cross-references: PDB:2AR9
Protein: DP02860 (UniProt P55211)
Region: residues 316	to 321
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In order to help elucidate the molecular mechanisms of cIAP1 activity and to explore the possibility of targeting cIAP1 activity with small molecules, we have determined the crystal structures of the BIR3 domain of cIAP1 in complex with N-terminal hexapeptides of the activated (cleaved) forms of both SMAC and caspase-9. 
Cross-references: PDB:3D9T
Protein: DP02860 (UniProt P55211)
Region: residues 316	to 321
Annotation: protein binding (Molecular function)
Evidence: surface plasmon resonance evidence used in manual assertion
Supporting statements:
The caspase-9 peptide (ATPFQE) binds to the BIR3 domain of cIAP2 with an afﬁnity of 48 ± 2nM, whereas the SMAC peptide (AVPIAQ) binds with an afﬁnity of 85 ± 8nM.
Protein: DP02862 (UniProt P08670)
Region: residues 99	to 144
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Surprisingly, a clear electron density is only observed starting from residues 144 and 149 in chains A and B, respectively. Moreover, SDS-PAGE analysis of the crystals confirmed that the fragment was intact (mass 11.1 kDa). In addition, first few traceable residues in each chain are mobile, as evident from increased B-factors. Both the coil 1A and most of the linker L1 are therefore completely disordered in this crystal structure.
With the exception of residues 144 to 149 (shown in orange) in chain A, the rest of the linker L1 and coil 1A is disordered in the crystals.
Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.
Coil 1A corresponds to region 99-139 and linker L1 corresponds to region 140-147.
Cross-references: PDB:3SSU
Protein: DP02862 (UniProt P08670)
Region: residues 99	to 144
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
Surprisingly, a clear electron density is only observed starting from residues 144 and 149 in chains A and B, respectively. Moreover, SDS-PAGE analysis of the crystals confirmed that the fragment was intact (mass 11.1 kDa). In addition, first few traceable residues in each chain are mobile, as evident from increased B-factors. Both the coil 1A and most of the linker L1 are therefore completely disordered in this crystal structure.
With the exception of residues 144 to 149 (shown in orange) in chain A, the rest of the linker L1 and coil 1A is disordered in the crystals.
Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.
Coil 1A corresponds to region 99-139 and linker L1 corresponds to region 140-147.
Cross-references: PDB:3SSU
Protein: DP02862 (UniProt P08670)
Region: residues 99	to 144
Annotation: molecular adaptor activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Surprisingly, a clear electron density is only observed starting from residues 144 and 149 in chains A and B, respectively. Moreover, SDS-PAGE analysis of the crystals confirmed that the fragment was intact (mass 11.1 kDa). In addition, first few traceable residues in each chain are mobile, as evident from increased B-factors. Both the coil 1A and most of the linker L1 are therefore completely disordered in this crystal structure.
With the exception of residues 144 to 149 (shown in orange) in chain A, the rest of the linker L1 and coil 1A is disordered in the crystals.
Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.
Coil 1A corresponds to region 99-139 and linker L1 corresponds to region 140-147.
Cross-references: PDB:3SSU
Protein: DP02863 (UniProt P62558)
Region: residues 272	to 323
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
SopB is a multidomain protein, which like P1 ParB contains an all-helical DNA-binding domain that is flexibly attached to a compact (β3–α)2 dimer-domain.
However, density was only observed for SopB residues 157–271 from one subunit and 157–270 of the second subunit. These residues contain all the determinants required for sequence specific binding to the sopC consensus site (36). The absence of density for the SopB N- and C-terminal regions suggested that either these regions were highly flexible or were proteolysed during crystallization. Consistent with the former possibility, the first and last residues observed, 157 and 271, each face into large solvent channels, which could easily accommodate the disordered or flexibly attached domains.
The structure indicates that SopB consists of three main regions: 1–155, 155–272 and 272–323 that are flexibly linked.
The fact that the N- and C-terminal regions are not visible in the FL SopB-18mer structure indicates that these three principal regions of SopB are flexibly attached.
The C-terminal dimerization domain of SopB is highly flexible.
Cross-references: PDB:3MKY
Protein: DP02863 (UniProt P62558)
Region: residues 275	to 323
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Previous studies suggest that SopB residues 275–323 are involved in dimer formation and therefore must form a folded domain, consistent with our CD studies (36). Thus, we next produced and crystallized SopB(275–323).
The structure revealed that, indeed, residues 275–323 form a highly intertwined dimer composed of 3 β-strands and 1 α-helix with topology (β1; 276–281, β2; 284–289, β3; 292–298 α1; 306–318) (Figure 2A–D). The dimer is stabilized almost entirely by backbone, β-strand hydrogen bonds. The interface of the dimer buries an extensive 5990 Å2 of protein surface from solvent, consistent with it forming the primary dimerization domain of SopB, which anchors the SopB subunits on a palindromic DNA site (see Figure 3). That the C-domain is a physiologically relevant oligomer is also supported by the finding that the identical dimer is observed twice in the crystal (the dimers overlay with an RMSD of 0.6 Å) and size exclusion chromatography data providing a MW of 13 kDa for SopB(275–323) [compared to a calculated MW of 11.2 kDa for a SopB(275–323) dimer].
Cross-references: PDB:3KZ5
Protein: DP02863 (UniProt P62558)
Region: residues 275	to 323
Annotation: disorder to order (Structural transition)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Previous studies suggest that SopB residues 275–323 are involved in dimer formation and therefore must form a folded domain, consistent with our CD studies (36). Thus, we next produced and crystallized SopB(275–323).
The structure revealed that, indeed, residues 275–323 form a highly intertwined dimer composed of 3 β-strands and 1 α-helix with topology (β1; 276–281, β2; 284–289, β3; 292–298 α1; 306–318) (Figure 2A–D). The dimer is stabilized almost entirely by backbone, β-strand hydrogen bonds. The interface of the dimer buries an extensive 5990 Å2 of protein surface from solvent, consistent with it forming the primary dimerization domain of SopB, which anchors the SopB subunits on a palindromic DNA site (see Figure 3). That the C-domain is a physiologically relevant oligomer is also supported by the finding that the identical dimer is observed twice in the crystal (the dimers overlay with an RMSD of 0.6 Å) and size exclusion chromatography data providing a MW of 13 kDa for SopB(275–323) [compared to a calculated MW of 11.2 kDa for a SopB(275–323) dimer].
Cross-references: PDB:3KZ5
Protein: DP02863 (UniProt P62558)
Region: residues 275	to 323
Annotation: self-assembly (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Previous studies suggest that SopB residues 275–323 are involved in dimer formation and therefore must form a folded domain, consistent with our CD studies (36). Thus, we next produced and crystallized SopB(275–323).
The structure revealed that, indeed, residues 275–323 form a highly intertwined dimer composed of 3 β-strands and 1 α-helix with topology (β1; 276–281, β2; 284–289, β3; 292–298 α1; 306–318) (Figure 2A–D). The dimer is stabilized almost entirely by backbone, β-strand hydrogen bonds. The interface of the dimer buries an extensive 5990 Å2 of protein surface from solvent, consistent with it forming the primary dimerization domain of SopB, which anchors the SopB subunits on a palindromic DNA site (see Figure 3). That the C-domain is a physiologically relevant oligomer is also supported by the finding that the identical dimer is observed twice in the crystal (the dimers overlay with an RMSD of 0.6 Å) and size exclusion chromatography data providing a MW of 13 kDa for SopB(275–323) [compared to a calculated MW of 11.2 kDa for a SopB(275–323) dimer].
Cross-references: PDB:3KZ5
Protein: DP02864 (UniProt P83917)
Region: residues 79	to 103
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis of MoMOD1 revealed two regions that are resistant to digestion, these correspond to the conserved sequences in the HP1-like proteins[…] The results suggest that the MoMOD1 protein consists of two structural domains, residues 10-78 and 104-171, connected by an exposed linker.
Protein: DP02864 (UniProt P83917)
Region: residues 79	to 103
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Limited proteolysis of MoMOD1 revealed two regions that are resistant to digestion, these correspond to the conserved sequences in the HP1-like proteins[…] The results suggest that the MoMOD1 protein consists of two structural domains, residues 10-78 and 104-171, connected by an exposed linker.
Protein: DP02865 (UniProt P05205)
Region: residues 131	to 140
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 By combining results of NMR and crystallography, we conclude that the CSD module is made up of residues 141 through 201 in the HP1a.
Cross-references: PDB:3P7J
Protein: DP02865 (UniProt P05205)
Region: residues 131	to 140
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
By measuring the heteronuclear NOE (Nuclear Overhauser Effect) data for backbone amides, we identified disordered regions, which exist at the N-terminus (residues 131 to 140 of intact HP1a), and the CTE (residues 202 to 206), as well as segments within the CSD module (residues 158–159, 162, 170, and 172–173) (Figure 3A).
Protein: DP02866 (UniProt A1Z9S6)
Region: residues 2415	to 2512
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
we identified an LCVKI motif in HP2 that binds to the HP1a CSD. The binding affinity of the HP2 fragment is approximately two orders of magnitude higher than that of peptides from PIWI (with a PRVKV motif), AF10 (with a PLVVL motif), or CG15356 (with LYPLL and LSIVA motifs). 
To investigate the hypothesis that tertiary structure in HP2 [10] is required for binding, we performed the reciprocal experiment, examining the 2D [15N-1H] HSQC spectrum of the 15N labeled HP2 fragment in the presence of unlabeled CSD (Figure 1C). We find that in the absence of the CSD the HP2 fragment is disordered. Both 1D 1H and 2D [15N-1H] HSQC spectra lack chemical shift dispersion. In the presence of the CSD, a limited set of resonances become perturbed (Figure 1C)
Protein: DP02866 (UniProt A1Z9S6)
Region: residues 2415	to 2512
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
we identified an LCVKI motif in HP2 that binds to the HP1a CSD. The binding affinity of the HP2 fragment is approximately two orders of magnitude higher than that of peptides from PIWI (with a PRVKV motif), AF10 (with a PLVVL motif), or CG15356 (with LYPLL and LSIVA motifs). 
To investigate the hypothesis that tertiary structure in HP2 [10] is required for binding, we performed the reciprocal experiment, examining the 2D [15N-1H] HSQC spectrum of the 15N labeled HP2 fragment in the presence of unlabeled CSD (Figure 1C). We find that in the absence of the CSD the HP2 fragment is disordered. Both 1D 1H and 2D [15N-1H] HSQC spectra lack chemical shift dispersion. In the presence of the CSD, a limited set of resonances become perturbed (Figure 1C)
Protein: DP02866 (UniProt A1Z9S6)
Region: residues 2415	to 2512
Annotation: molecular function regulator (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
we identified an LCVKI motif in HP2 that binds to the HP1a CSD. The binding affinity of the HP2 fragment is approximately two orders of magnitude higher than that of peptides from PIWI (with a PRVKV motif), AF10 (with a PLVVL motif), or CG15356 (with LYPLL and LSIVA motifs). 
To investigate the hypothesis that tertiary structure in HP2 [10] is required for binding, we performed the reciprocal experiment, examining the 2D [15N-1H] HSQC spectrum of the 15N labeled HP2 fragment in the presence of unlabeled CSD (Figure 1C). We find that in the absence of the CSD the HP2 fragment is disordered. Both 1D 1H and 2D [15N-1H] HSQC spectra lack chemical shift dispersion. In the presence of the CSD, a limited set of resonances become perturbed (Figure 1C)
Protein: DP02866 (UniProt A1Z9S6)
Region: residues 2415	to 2512
Annotation: molecular function regulator (Molecular function)
Evidence: fluorescence polarization evidence used in manual assertion
Supporting statements:
we identified an LCVKI motif in HP2 that binds to the HP1a CSD. The binding affinity of the HP2 fragment is approximately two orders of magnitude higher than that of peptides from PIWI (with a PRVKV motif), AF10 (with a PLVVL motif), or CG15356 (with LYPLL and LSIVA motifs). 
To determine the affinity of HP2 for the HP1a CSD we performed fluorescence polarization assays. We designed a short HP2 peptide (22 aa) with the critical valine residue near the center […] Using this assay, we observed that both HP2 and PIWI binding are shifted to the millimolar range by I191E and W200A mutations in HP1a. Thus, both peptides bind using a similar mechanism; they bind to the CSD dimer and require the PXVXL platform (Figure 4A).
Protein: DP02867 (UniProt P40381)
Region: residues 1	to 74
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
HP1Swi6 consists of four domains: An N-terminal domain (NTD, residues 1–74), which is presumably flexibly disordered; a chromodomain (CD, residues 75–139), which binds K9-methylated histone tails (Bannister et al., 2001); a hinge region (H, residues 140–264); and a C-terminal chromo shadow domain (CSD, residues 265–328) (Cowieson et al., 2000).
The chemical shift dispersion and intensities of the resonances in full-length HP1Swi6 indicated the CD and the CSD to be folded domains and the NTD and the hinge region to be flexibly unfolded polypeptide segments, as expected from predictions of the secondary structure.
Protein: DP02867 (UniProt P40381)
Region: residues 140	to 264
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
HP1Swi6 consists of four domains: An N-terminal domain (NTD, residues 1–74), which is presumably flexibly disordered; a chromodomain (CD, residues 75–139), which binds K9-methylated histone tails (Bannister et al., 2001); a hinge region (H, residues 140–264); and a C-terminal chromo shadow domain (CSD, residues 265–328) (Cowieson et al., 2000).
The chemical shift dispersion and intensities of the resonances in full-length HP1Swi6 indicated the CD and the CSD to be folded domains and the NTD and the hinge region to be flexibly unfolded polypeptide segments, as expected from predictions of the secondary structure.
Protein: DP02867 (UniProt P40381)
Region: residues 140	to 264
Annotation: RNA binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
By using NMR chemical shift titrations monitored on amide resonances in the flexible hinge region, we determined the binding constant of full-length HP1Swi6 to a 20-mer RNA as 38 ± 13 μM (Figure 3C). These results demonstrate that HP1Swi6 is able to bind RNA alone and that the hinge region is substantially involved in this binding interaction.
Protein: DP02867 (UniProt P40381)
Region: residues 140	to 264
Annotation: RNA binding (Molecular function)
Evidence: electrophoretic mobility shift assay evidence used in manual assertion
Supporting statements:
To test whether the hinge region also confers RNA binding properties to HP1Swi6, we purified recombinant CD, hinge, and CSD. In contrast to the CD and the CSD, the isolated hinge region was sufficient for strong RNA binding (Figure 3B).
Protein: DP02868 (UniProt Q9Y5S9)
Region: residues 50	to 63
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although Y14 residues 50–168 are present in the Y14t-Magoh complex crystals, only residues 64–165 are sufficiently well ordered to be visualized in the electron density.
Cross-references: PDB:1P27
Protein: DP02869 (UniProt Q16630)
Region: residues 13	to 80
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although diffraction data were collected from a complex containing residues 13-235 of CFIm68 (Figure S2B), the refined electron density map showed interpretable density only for residues 81-172, a segment which comprises the entire RRM domain (residues 81-160).
Cross-references: PDB:3Q2S
PDB:3Q2T
Protein: DP02869 (UniProt Q16630)
Region: residues 173	to 235
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although diffraction data were collected from a complex containing residues 13-235 of CFIm68 (Figure S2B), the refined electron density map showed interpretable density only for residues 81-172, a segment which comprises the entire RRM domain (residues 81-160).
Cross-references: PDB:3Q2S
PDB:3Q2T
Protein: DP02869 (UniProt Q16630)
Region: residues 481	to 519
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Similar to the TNPO3-SRSF1 co-crystal structure, only a fraction of the input CPSF6 RSLD (9 of the 70 residues) was ordered in the density map.
Cross-references: PDB:6GX9
Protein: DP02869 (UniProt Q16630)
Region: residues 531	to 550
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Similar to the TNPO3-SRSF1 co-crystal structure, only a fraction of the input CPSF6 RSLD (9 of the 70 residues) was ordered in the density map.
Cross-references: PDB:6GX9
Protein: DP02869 (UniProt Q16630)
Region: residues 492	to 496
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
Four sites in the RSLD, Ser494, Ser500, Ser511 and Ser513, were phosphorylated in both endogenous CPSF6 and exogenously expressed CPSF6[551] protein.
Includes the phosphorylated Ser494.
Protein: DP02869 (UniProt Q16630)
Region: residues 498	to 502
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
Four sites in the RSLD, Ser494, Ser500, Ser511 and Ser513, were phosphorylated in both endogenous CPSF6 and exogenously expressed CPSF6[551] protein.
Includes the phosphorylated Ser500.
Protein: DP02869 (UniProt Q16630)
Region: residues 509	to 515
Annotation: phosphorylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
Four sites in the RSLD, Ser494, Ser500, Ser511 and Ser513, were phosphorylated in both endogenous CPSF6 and exogenously expressed CPSF6[551] protein.
Includes the phosphorylated Ser511 and Ser513.
Protein: DP02869 (UniProt Q16630)
Region: residues 481	to 551
Annotation: localization (Biological process)
Evidence: microscopy evidence used in manual assertion
Supporting statements:
The RSLD confers CPSF6 nuclear import without any contribution from PY-NLS