LiteFold/DisProt huggingface dataset:
Protein: DP00887 (UniProt P21246)
Region: residues 144	to 168
Annotation: molecular function activator activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
PTN112–136 inhibited binding of PTN to anb3 integrin, and as shown by surface plasmon resonance (SPR) measurements, specifically interacted with the specificity loop of the extracellular domain of b3. Moreover, it abolished PTN-induced FAK Y397 phosphorylation, similarly to the effect of a neutralizing anb3-selective antibody
PTN112_136 AFFECTED THE INTERACTION OF PTN WITH  anb3 INTEGRIN. Since both RPTPb/z and anb3 integrin are required for PTN-induced HUVEC migration [Polykratis et al., 2005; Mikelis et al., 2009], we studied whether PTN112–136 affects interaction of PTN with alphav b3, RPTPb/z, or both. Cells were grown in the presence or absence of PTN112–136 and in each case, 3mg of total protein from cell lysates were immunoprecipitated for anb3 or RPTPb/z and analyzed for the presence of PTN. PTN112–136 inhibited interaction of PTN with anb3 (Fig. 3A) but not RPTPb/z (Fig. 3B) in HUVEC.
In the present study, we show that the C-terminal region of PTN is responsible for binding to the Cys-loop of the b3 subunit, playing a major role in the interaction of PTN with anb3 and the resulting stimulation of cell migration.
The numbering by the authors differs from the uniprot numbering. Residue 112-136 correspond to 144-168 of the uniprot numbering.
Protein: DP00887 (UniProt P21246)
Region: residues 144	to 168
Annotation: self-activation (Disorder function)
Evidence: enzyme-linked immunoabsorbent assay evidence used in manual assertion
Supporting statements:
PTN112–136 inhibited binding of PTN to anb3 integrin, and as shown by surface plasmon resonance (SPR) measurements, specifically interacted with the specificity loop of the extracellular domain of b3. Moreover, it abolished PTN-induced FAK Y397 phosphorylation, similarly to the effect of a neutralizing anb3-selective antibody
Collectively, our data suggest that although PTN112–136 induces some of the signaling pathways triggered by PTN, it inhibits PTN-induced angiogenic activities through inhibition of PTN binding to anb3 integrin. 
Based on the assumption that integrin-dependent Y397 autophosphorylation of FAK is the first step of its activation [Mitra and Schlaepfer, 2006], we studied whether PTN affects Y397 phosphorylation of FAK through anb3, as well as the effect of PTN112–136. As shown in Figure 5, PTN at the concentration of 100 ng/ml that causes the maximal effect on HUVEC migration [Polykratis et al., 2005], induced Y397 FAK auto-phosphorylation, an effect completely abolished by the anb3 neutralizing antibody LM609 or by PTN112–136
PTN induces Y397 FAK phosphorylation through anb3, an effect completely abolished by PTN112–136. FAK activation is required for integrin-mediated cell migration [Sieg et al., 1999] and the autophopshorylation on Y397 is prerequisite for the subsequent binding and activation from c-src [Mitra et al., 2005]. It seems that PTN binding to the cysteine loop 177–184 of anb3 leads to the initial activation of FAK, its interaction with the activated c-src and the induction of the migratory response, and PTN112–136 blocks this process (Fig. 8).
The numbering by the authors differs from the uniprot numbering. Residue 112-136 correspond to 144-168 of the uniprot numbering.
Protein: DP00887 (UniProt P21246)
Region: residues 144	to 168
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
NMR spectroscopy studies showed that PTN112–136 was characterized by conformational flexibility and absence of any element of secondary structure at room temperature, although the biologically active peptide segment 123–132 may adopt a defined structure at lower temperature.
The NMR data for PTN112–136 suggest a conformation with no well-defined secondary structure elements for this peptide, due to the absence of any long-range and the limited number of medium-range (i,i.3) NOEs (Fig. 7B). However, a backbone bend is formed by residues Glu127–Gln131, indicating the formation of a segment with local folded structure in the conformational ensemble (Fig. 7C). As far as the nature of the peptide bond for both prolines is concerned, analysis of the proline 13C resonances observed for PTN112–136, demonstrate in both cases, Pro115 and Pro117, the existence of a dominant trans conformation. Cb of Pro115 is found to be at 33.172 ppm, while Cg is found at 29.632 ppm. The difference in ppm is 3.54, indicating that
the dominant conformation of the Lys114–Pro115 peptide bond of the model ensemble is trans and that cis–trans isomerization is not detectable in NMR time scale. The corresponding Dbg value for Pro117 is found to be 4.021, suggesting a trans conformation for the peptide bond between residues Lys116–Pro117

Based on the assumption that integrin-dependent Y397 autophosphorylation of FAK is the first step of its activation [Mitra and Schlaepfer, 2006], we studied whether PTN affects Y397 phosphorylation of FAK through anb3, as well as the effect of PTN112–136. As shown in Figure 5, PTN at the concentration of 100 ng/ml that causes the maximal effect on HUVEC migration [Polykratis et al., 2005], induced Y397 FAK auto-phosphorylation, an effect completely abolished by the anb3 neutralizing antibody LM609 or by PTN112–136
In an effort to better characterize PTN112–136 and to identify the
likely minimum amino acid sequence involved in its biological
activity, we elucidated the structural features of PTN112–136 by NMR
spectroscopy. The peptide proved to be highly flexible in solution at
room temperature.
The numbering by the authors differs from the uniprot numbering. Residue 112-136 correspond to 144-168 of the uniprot numbering.
Protein: DP00889 (UniProt P9WF19)
Region: residues 1	to 45
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here we present the first crystal structure of a prokaryotic VapBC complex, VapBC-5 from M. tuberculosis. The toxin, VapC-5, contains 126 residues (Mr 14.0 kDa) and the antitoxin, VapB-5, contains 34 residues (Mr 3.8 kDa)
The structure of VapB-5 antitoxin shows clear electron density for 33 residues out of 93 (86 native and seven from the vector). The missing residues are part of the N-terminal region that is predicted to bind to DNA
Cross-references: PDB:3DBO
Protein: DP00893 (UniProt P08240)
Region: residues 130	to 176
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered parts of the complex are indicated by dashed lines.
Residues 41X-47X, 131X-176X, 208B-219B, and 248B-254B are not ordered and therefore missing in the model.
Cross-references: PDB:2FH5
Protein: DP00893 (UniProt P08240)
Region: residues 131	to 176
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the Electron Microscopy structure of the signal recognition particle receptor (SR) in complex with signal recognition particle (SRP) and ribosome nascent chain complex
Cross-references: PDB:2GO5
EMDB:1217
Protein: DP00893 (UniProt P08240)
Region: residues 130	to 238
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density in the Electron Microscopy structure of the Mammalian ribosome nascent chain complex with SRP and SRP receptor in early state A.
Cross-references: EMDB:12303
PDB:7NFX
Protein: DP00895 (UniProt P03421)
Region: residues 1	to 102
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The monomeric PN fragment displayed a CD spectrum at 25 °C typical of a disordered conformation with a predominant minimum at ∼200 nm, no components of regular secondary structure, and the expected increase in secondary structure content at high temperature due to strengthening of hydrophobic interactions, a typical feature of IDP regions (Figure 2C).
Protein: DP00895 (UniProt P03421)
Region: residues 1	to 102
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The monomeric PN and PC fragments presented ratios (MWSEC/MWSLS) of 2.7 ± 0.1 and 3.1 ± 0.1, respectively, which can be explained by the extended conformation and low compactness of the polypeptide chain typical of IDPs.
Protein: DP00895 (UniProt P03421)
Region: residues 162	to 241
Annotation: disorder (Structural state)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
The monomeric PN and PC fragments presented ratios (MWSEC/MWSLS) of 2.7 ± 0.1 and 3.1 ± 0.1, respectively, which can be explained by the extended conformation and low compactness of the polypeptide chain typical of IDPs.
Protein: DP00895 (UniProt P03421)
Region: residues 162	to 241
Annotation: pre-molten globule (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The monomeric PC fragment presented a CD spectrum characterized by a small negative band at 220 nm indicative of some degree of α-helical content and a minimum centered at 204 nm, which indicates a mixture of contributions from disorder (200 nm) and α-helix (208 nm), showing that PC features both structured and disordered elements in contrast to the fully disordered conformation of the PN fragment (Figure 2F).
Thermal denaturation of full-length P revealed a structural transition between 5 and 60 °C, with some degree of cooperativity (Figure 4A, top panel). Within this temperature range, PTET, PNTET, and PN showed no thermal transition (Figure 4A, bottom panel) while PC and PTETC showed transitions similar to that of P (Figure 4B), in accordance with the results depicted in Figure 2.
 In particular at pH 3.0, the PC fragment (pI = 4.34) presented an increase in α-helical content (Figure 8A), which resulted in substantial compaction of PC as determined by SEC, changing the MWSEC/MWSLS ratio from 3.1 ± 0.2 to 1.3 ± 0.1, similar to that of a globular protein (Figure 8B).
These findings supported the pre-molten globule-like nature of the PC module, whereas charge neutralization drives the extended structure to adopt a globular fold with a high degree of α-helical content.
Protein: DP00895 (UniProt P03421)
Region: residues 1	to 118
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
With the protein digestion protocol we used (see Experimental Procedures), we obtained a major species of fragment Y of 4959.6 Da determined by mass spectrometry, which fits well with a peptide containing three additional residues (Ser-Ala-Arg) in the carboxy terminal region (peptide starting at Ser 119 and ending at Arg 163 with a theoretical mass of 4958.4 Da).
Protein: DP00895 (UniProt P03421)
Region: residues 164	to 241
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
With the protein digestion protocol we used (see Experimental Procedures), we obtained a major species of fragment Y of 4959.6 Da determined by mass spectrometry, which fits well with a peptide containing three additional residues (Ser-Ala-Arg) in the carboxy terminal region (peptide starting at Ser 119 and ending at Arg 163 with a theoretical mass of 4958.4 Da).
Protein: DP00895 (UniProt P03421)
Region: residues 161	to 241
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Therefore, P protein was doubly digested with a mixture of sequencing grade trypsin and chymotrypsin. This was followed by gel filtration chromatography, as described previously for fragment X. A peak eluting as a ∼120 kDa species showed a single band of ∼9 kDa in a SDS-PAGE gel [labeled Y* in Fig. 5(B)], that migrated faster than fragment X.
Protein: DP00895 (UniProt P03421)
Region: residues 1	to 118
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Therefore, P protein was doubly digested with a mixture of sequencing grade trypsin and chymotrypsin. This was followed by gel filtration chromatography, as described previously for fragment X. A peak eluting as a ∼120 kDa species showed a single band of ∼9 kDa in a SDS-PAGE gel [labeled Y* in Fig. 5(B)], that migrated faster than fragment X.
Protein: DP00895 (UniProt P03421)
Region: residues 234	to 241
Annotation: protein binding (Molecular function)
Evidence: glutathione S-transferase pull-down assay evidence used in manual assertion
Supporting statements:
We then shortened the P230–241 region at either end and produced the corresponding GST–P proteins in E. coli. Mutants PΔN231, PΔN232 and PΔN233 – the latter retaining only the nine most C-terminal amino acids of P – were still able to pull down N with the same efficiency as PΔN230 (Fig. 6c, dF6).
On the other hand, removal of the very C-terminal amino acid of P completely abolished its capacity to pull down N, just like the other mutants tested lacking 2 or 3 aa from the C terminus (Fig. 6c, dF6). Thus, the C-terminal P segment spanning aa 234–241 appears to contain the minimal region for efficient interaction with RNA–N in this system.
Protein: DP00895 (UniProt P03421)
Region: residues 161	to 241
Annotation: protein binding (Molecular function)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
In order to characterize and compare the complexes co-purified by using either the oligomeric full-length P or the C-terminal fragment PΔN161, the samples were analysed by negative-staining electron microscopy (EM) after proteolytic separation from GST. Fig. 2F2(a, b) shows nucleocapsid-like structures eluted from GST beads for both P–N (a) and PΔN161–N (b).
Protein: DP00895 (UniProt P03421)
Region: residues 161	to 241
Annotation: disorder (Structural state)
Evidence: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence used in manual assertion
Supporting statements:
The second peak (P3), which eluted at 16.9 ml, only absorbed at 220 nm and contained the PΔN161 fragment. Its apparent mass was between 20.2 and 47.2 kDa, higher than its predicted mass of 10 kDa, presumably due to a markedly non-globular shape of the fragment (Tarbouriech et al., 2000).
Protein: DP00895 (UniProt P03421)
Region: residues 161	to 241
Annotation: viral life cycle (Biological process)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
In order to characterize and compare the complexes co-purified by using either the oligomeric full-length P or the C-terminal fragment PΔN161, the samples were analysed by negative-staining electron microscopy (EM) after proteolytic separation from GST. Fig. 2F2(a, b) shows nucleocapsid-like structures eluted from GST beads for both P–N (a) and PΔN161–N (b).
Protein: DP00895 (UniProt P03421)
Region: residues 234	to 241
Annotation: viral life cycle (Biological process)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
We then shortened the P230–241 region at either end and produced the corresponding GST–P proteins in E. coli. Mutants PΔN231, PΔN232 and PΔN233 – the latter retaining only the nine most C-terminal amino acids of P – were still able to pull down N with the same efficiency as PΔN230 (Fig. 6c, dF6).
On the other hand, removal of the very C-terminal amino acid of P completely abolished its capacity to pull down N, just like the other mutants tested lacking 2 or 3 aa from the C terminus (Fig. 6c, dF6). Thus, the C-terminal P segment spanning aa 234–241 appears to contain the minimal region for efficient interaction with RNA–N in this system.
Protein: DP00898 (UniProt P13338)
Region: residues 1	to 31
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The entire β-flap was built into the electron density map, but there was no clear density for two terminal segments of gp33, so only residues 32–102 (of the full 112) were modeled in the structure (Fig. 1). Analysis of the crystals indicated that they contained both proteins without proteolytic degradation (Fig. S1C), so the N-terminal 31 and C-terminal 10 residues of gp33 are presumed disordered in the crystals.
Cross-references: PDB:3TBI
Protein: DP00898 (UniProt P13338)
Region: residues 103	to 112
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The entire β-flap was built into the electron density map, but there was no clear density for two terminal segments of gp33, so only residues 32–102 (of the full 112) were modeled in the structure (Fig. 1). Analysis of the crystals indicated that they contained both proteins without proteolytic degradation (Fig. S1C), so the N-terminal 31 and C-terminal 10 residues of gp33 are presumed disordered in the crystals.
Cross-references: PDB:3TBI
Protein: DP00901 (UniProt O75496)
Region: residues 70	to 91
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
N-terminal residues 70-91 were not visible in the electron density maps using the experimental phases, calculated at different range of resolution. To determine whether these residues were lost by proteolysis, SDS-PAGE and Mass Spectroscopy were used to analyze the geminin 70-152 peptide in the crystals. The mass of the peptide in geminin 70-152 crystal was 13162.64 D and the peptide in Selenomethionine geminin 70-152 crystal was 13394.44 D, suggesting that the crystallized peptides were intact without any degradation. Therefore residues 70-91 of geminin are disordered and not observed in the electron density map.
Cross-references: PDB:1UII
Protein: DP00903 (UniProt P47813)
Region: residues 1	to 25
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Amino acids 1–24 and 118–143 at each terminus, as well as the His tag, do not have any observable long-range NOEs and have dynamics indicative of random coil conformations (data not shown).
Authors are not considering the first M residue, thus the disorder region is 1-25.
Cross-references: PDB:1D7Q
BMRB:4519
Protein: DP00903 (UniProt P47813)
Region: residues 119	to 144
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Amino acids 1–24 and 118–143 at each terminus, as well as the His tag, do not have any observable long-range NOEs and have dynamics indicative of random coil conformations (data not shown).
Authors are not considering the first Met residue, thus the disorder region is 119-144.
Cross-references: PDB:1D7Q
BMRB:4519
Protein: DP00903 (UniProt P47813)
Region: residues 1	to 27
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The NTT of eIF1A is not observed (residues 1–27) together with several loop regions (residues 54–56; 97–100; 109–112) (Figure 1A and B).
Cross-references: PDB:3ZJY
Protein: DP00903 (UniProt P47813)
Region: residues 129	to 144
Annotation: protein binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Deletion of eIF1A-CT16 affects a distinct surface on eIF1A-OB, which is a subset of that affected by deletion of eIF1A-CTT (compare Figure ​2B and Supplementary Figure S1A). Adding eIF1A-CT16 to 15N-labeled eIF1AΔC or eIF1AΔNC affects most of the same surfaces affected by the respective deletion (data not shown). Therefore, eIF1A-CT16 contacts the OB domain at a specific surface.
Protein: DP00903 (UniProt P47813)
Region: residues 138	to 144
Annotation: protein binding (Molecular function)
Evidence: competitive binding evidence used in manual assertion
Supporting statements:
The affinity of Fl-eIF1A-CT7 for eIF5B-D4 was 12 μM. Competition FA assays using Fl-eIF1A-CT7 showed that the binding affinities of eIF1A-CT16 (12 μM) and of the full 26-residue eIF1A-CTT (12 μM) were similar (Figure ​3A and B, Table 1). In contrast, the affinity of full-length eIF1A for eIF5B-D4 was 39 μM, much weaker than that of eIF1A-CTT (Figure ​3B and Table ​1).
Protein: DP00908 (UniProt P9WJ35)
Region: residues 1	to 46
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
For VapB30, we were unable to build the residues Met1–Val46 and residues Tyr77–Ala84 because of ambiguous or missing electron density in crystal form II. In crystal form I, the electron density of the residues Met1–Val46 was also absent; however, additional residues (Tyr77–Glu79) in chains B and H were visible in the electron density map.
Cross-references: PDB:4XGQ
PDB:4xgr
Protein: DP00913 (UniProt A0A0J9X1Q5)
Region: residues 746	to 764
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
no electron density visible for residues from 745 to 765 of chain A and 743 to 765 of chain B, respectively
Cross-references: PDB:4PPM
Protein: DP00913 (UniProt A0A0J9X1Q5)
Region: residues 1	to 371
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Surprisingly, the final model contains only 481 amino acids, including residues from Ala372 to Asp853, no electron density visible for the fragment from residues Met1 to Ala371.
In the final model, both monomers include the residues from 372 to 853, but no electron density visible for residues from 745 to 765 of chain A and 743 to 765 of chain B, respectively.
Sequence analysis showed that the C terminal of PigE (residue 372–853) is the putative catalytic domain, which shares some homology with the PLP-dependent aminotransferase family proteins, but the function for the N-terminal domain (residue 1–371) is unclear.
Cross-references: PDB:4PPM
Protein: DP00919 (UniProt C6KEI3)
Region: residues 152	to 180
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The PXXP motif in the present structure is from residues 74–80 while the 30-residue disordered loop distal to this motif ranges from residues 151–180.
There are two structural analysis in the PDB showing disorder regions:151-180 and 152-180. 152-180 comprises both structural analysis
Cross-references: PDB:2XI1
Protein: DP00919 (UniProt C6KEI3)
Region: residues 1	to 75
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
On the other hand, the N-terminal anchor domain is disordered in the full-length structure.
Crystal diffraction and poor reproducibility were problems faced during the experiments and in hindsight were probably due to the disordered N-terminal domain as explained in ‘Results’.
Cross-references: PDB:2XI1