LiteFold/DisProt huggingface dataset:
Protein: DP03614 (UniProt Q7DDR9)
Region: residues 178	to 191
Annotation: self-regulatory activity (Disorder function)
Evidence: ATP bioluminescence assay evidence used in manual assertion
Supporting statements:
We have shown that cis-autoadenylylation of NmFic constitutes an in-built mechanism to covalently modify Y183, resulting in partial unfolding of the αinh.
Thus, to test for any functional role of Y183, we removed its hydroxyl group by introducing an additional Y183F mutation into the alleles of active (i.e., oligomerization-deficient), mutants. Strikingly, the mutation suppressed the growth defect phenotype as efficiently as mutation of the catalytic His (H107A) (Fig. 3A, Right), suggesting a crucial regulatory role for Y183.
Similarly, NmFicE156R,Y183F shows autoadenylylation, although with a considerably slower rate (Fig. 3 D and G). Such an effect of the Y183F mutation was also observed for NmFicmono,Y183F by MS (Fig. S6B). As mentioned above, the modification on residues Y184, Y185, and Y188 is probably not of functional relevance.
Protein: DP03615 (UniProt A0A1Y0DDB3)
Region: residues 43	to 68
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two N-terminal residues and 11 C-terminal residues (residues 141–151) and residues of the loop 43–68 could not be modelled due to missing/ambiguous electron density. Significantly, this missing loop region is a common and recurring scenario observed in other NDK crystal structures in the PDB that have been crystallized in the absence of ligand, or when the ligand density is not observed suggesting that in the absence of ligand, this loop is flexible.
In the structure, regions corresponding to residues 43–68 and 141–151 of other NDKs were missing, a fact observed in other non-liganded NDK structures.
Cross-references: PDB:5GO1
Protein: DP03615 (UniProt A0A1Y0DDB3)
Region: residues 141	to 151
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Two N-terminal residues and 11 C-terminal residues (residues 141–151) and residues of the loop 43–68 could not be modelled due to missing/ambiguous electron density. Significantly, this missing loop region is a common and recurring scenario observed in other NDK crystal structures in the PDB that have been crystallized in the absence of ligand, or when the ligand density is not observed suggesting that in the absence of ligand, this loop is flexible.
In the structure, regions corresponding to residues 43–68 and 141–151 of other NDKs were missing, a fact observed in other non-liganded NDK structures.
Cross-references: PDB:5GO1
Protein: DP03616 (UniProt Q9JZ10)
Region: residues 20	to 66
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
From R1 and R2 relaxation rates as well as heteronuclear Nuclear Overhauser Effects (NOE) we identified a loop region corresponding to residues 20–60, which is characterized by fast motions in the range of μs-ms within the otherwise rigid protein (Fig. 1, A and B).
Cross-references: PDB:2KXI
BMRB:16737
Protein: DP03616 (UniProt Q9JZ10)
Region: residues 55	to 59
Annotation: metal ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Another residue affected by iron binding is His-57.
Protein: DP03616 (UniProt Q9JZ10)
Region: residues 44	to 48
Annotation: metal ion binding (Molecular function)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Because of the diamagnetic nature of zinc-II, in contrast to paramagnetic iron-III, the spectra still show a good resolution, which allows the identification of the fourth metal-coordinating residue within NarE namely His-46.
Protein: DP03617 (UniProt Q7BMQ8)
Region: residues 1	to 42
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-termini residues M1 to S9 have not been assigned because of line broadening most likely due to solvent exchange and/or conformational exchange.
The remaining residues from 9 to 42 are described as disordered in Figure 2.
Cross-references: BMRB:17250
Protein: DP03619 (UniProt Q9NZD4)
Region: residues 92	to 102
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N-terminal 4 residues and the C-terminal 11 are unstructured in both conformations.
Cross-references: PDB:1W0B
Protein: DP03620 (UniProt Q12051)
Region: residues 310	to 322
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Each monomer of the refined structure encompassed 322 of the 335 total residues of the GGPPs sequence, with a small disordered region of residues 315–327.
The refined structure of type-III GGPPs in complex with one magnesium ion in each subunit contains amino acid residues 2-314 and 328–340. The electron density map between residues 315 and 327 at the C terminus is not clearly visible.
The IDR characterized in the publication and spanning residues 315-327 corresponds to region 310-322 of the amino acid sequence, since the authors included a five-residue sequence (MTKNK) between the N terminus of GGPPs and the Factor Xa cleavage sequence to expose the protease site for tag removal.
Cross-references: PDB:2DH4
Protein: DP03621 (UniProt P04807)
Region: residues 1	to 17
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model contains residues 18–486 and 442 water molecules. No continuous density can be observed for the first 17 residues of the N terminus. Yeast HK is susceptible to limited proteolysis by endogenous proteases, resulting in loss of the first 11 N-terminal amino acid residues (36, 37), which, together with the thermal disorder, is probably the reason for the lack of electron density at the N terminus.
Cross-references: PDB:1IG8
Protein: DP03621 (UniProt P04807)
Region: residues 13	to 17
Annotation: phosphorylation display site (Disorder function)
Evidence: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion
Supporting statements:
The principal and perhaps sole site of phosphorylation is now identified as residue serine-15, by observation of a single tryptic peptide difference, its sequencing and size determination by mass spectrometry, and by mutation to alanine, which prevents phosphorylation in vivo. Although protein kinase A was unlikely to accomplish the phosphorylation in vivo, serine-15 does belong to a protein kinase A consensus phosphorylation sequence, and in vitro phosphorylation by protein kinase A at serine-15 could be shown by labeling and by peptide determination. The alanine-15 mutant enzyme was not phosphorylated in vitro.
The present work shows by chemical identification and mutagenesis that for hexokinase 2 it is residue serine-15 which is phosphorylated in vivo in the regime employed. This residue, which is in a protein kinase A consensus sequence, Arg-Lys-Gly-Ser (Kennelly & Krebs, 1991; Denis et al., 1991; Gibbs et al., 1992), is also phosphorylated, albeit slowly, by protein kinase A in vitro, and the alanine-15 mutant protein (S15A) is not.
This is the expected result of the conversion of serine to serine phosphate, producing a derivative that cannot be efficiently extracted from the sequencing support by the apolar organic solvents employed (Meyer et al., 1991). Mass spectrometry of the two peptides, 1 and 2, respectively, showed the nonapeptide masses expected, 936.6 Da with serine unsubstituted and 1015.3 Da with phosphoserine (Figure 5).
This paper identifies serine-15 as a primary residue phosphorylated in vivo in yeast hexokinase 2. The loss of labeling in vivo in the alanine-15 mutant suggests it may even be the only site or be required for phosphorylation of other sites.
Protein: DP03621 (UniProt P04807)
Region: residues 13	to 17
Annotation: phosphorylation display site (Disorder function)
Evidence: site-directed mutagenesis phenotypic evidence used in manual assertion
Supporting statements:
The principal and perhaps sole site of phosphorylation is now identified as residue serine-15, by observation of a single tryptic peptide difference, its sequencing and size determination by mass spectrometry, and by mutation to alanine, which prevents phosphorylation in vivo. Although protein kinase A was unlikely to accomplish the phosphorylation in vivo, serine-15 does belong to a protein kinase A consensus phosphorylation sequence, and in vitro phosphorylation by protein kinase A at serine-15 could be shown by labeling and by peptide determination. The alanine-15 mutant enzyme was not phosphorylated in vitro.
The present work shows by chemical identification and mutagenesis that for hexokinase 2 it is residue serine-15 which is phosphorylated in vivo in the regime employed. This residue, which is in a protein kinase A consensus sequence, Arg-Lys-Gly-Ser (Kennelly & Krebs, 1991; Denis et al., 1991; Gibbs et al., 1992), is also phosphorylated, albeit slowly, by protein kinase A in vitro, and the alanine-15 mutant protein (S15A) is not.
In vivo labeling (Figure 6), i.e., the same regime but including 32P-inorganic phosphate, showed essentially no labeling of hexokinase 2(S15A) (size ~50 kDa) from either 2% or 0.1% glucose (lanes 3 and 4, respectively) as compared with the prominent labeling of the wild-type enzyme (lanes 1 and 2) in the same regime from 0.1% glucose.
Since the present results showed that the residue of hexokinase 2 phosphorylated in vivo was in fact serine-15, in vitro phosphorylation of the S15 A mutant enzyme was tested. Figure 7 (lower panel) shows phosphorylation of wild-type hexokinase 2 fraction HA-I (lanes 1 and 3), but not of fraction HA-II (lane 5), and no phosphorylation of hexokinase 2 mutant S15A (lanes 7 and 9).
This paper identifies serine-15 as a primary residue phosphorylated in vivo in yeast hexokinase 2. The loss of labeling in vivo in the alanine-15 mutant suggests it may even be the only site or be required for phosphorylation of other sites.
Protein: DP03622 (UniProt Q12962)
Region: residues 178	to 191
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered L2 loop of TAF10 is represented by a dotted line
The final model includes TAF8 residues 28–120 and TAF10 residues 113–212 with the exception of a flexible loop in TAF10 comprising residues 178–191
Cross-references: PDB:4WV4
Protein: DP03622 (UniProt Q12962)
Region: residues 178	to 191
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered L2 loop of TAF10 is represented by a dotted line
The final model includes TAF8 residues 28–120 and TAF10 residues 113–212 with the exception of a flexible loop in TAF10 comprising residues 178–191
Cross-references: PDB:4WV4
Protein: DP03622 (UniProt Q12962)
Region: residues 1	to 112
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy structure of the Human transcription factor IID (TFIID) complex shows this region of the subunit 10 lacks electron density, indicating it is disordered. 
Cross-references: PDB:6MZD
PDB:6MZC
PDB:6MZM
PDB:6MZL
Protein: DP03622 (UniProt Q12962)
Region: residues 178	to 191
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy structure of the Human transcription factor IID (TFIID) complex shows this region of the subunit 10 lacks electron density, indicating it is disordered. 
Cross-references: PDB:6MZD
PDB:6MZC
PDB:6MZM
PDB:6MZL
Protein: DP03622 (UniProt Q12962)
Region: residues 209	to 218
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy structure of the Human transcription factor IID (TFIID) complex shows this region of the subunit 10 lacks electron density, indicating it is disordered. 
Cross-references: PDB:6MZD
PDB:6MZC
PDB:6MZM
PDB:6MZL
Protein: DP03623 (UniProt P0DTC1)
Region: residues 4393	to 4405
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The Far-UV CD spectrum of nsp11 protein (theoretical molecular weight is 1.33 kDa) shows a signature minima at 200 nm (Fig. 1A), suggest the spectrum of typical disordered type protein.
Protein: DP03623 (UniProt P0DTC1)
Region: residues 4393	to 4405
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Analogous to lipid membranes, the SDS micelles used to mimic the interface between hydrophobic and hydrophilic environments such as the plasma membrane and the cytosol [34]. SDS is a denaturing detergent with folding inducing properties that form micelles (CMC is 1.99 mM in 50 mM phosphate buffer [35])
At higher concentrations (25, 50, and 100 mM) the CD spectra of nsp11 exhibited two minima at 206 and 222 nm suggesting the structural transition from the disordered to ordered conformation (Fig. 3A and B).
With increasing TFE concentration it is evident that the negative ellipticity at 200 nm becomes lesser and negative ellipticities at 208 nm and 222 nm become towards higher value (Fig. 2A and B). The change in the ellipticity at the corresponding wavelength indicates that nsp11 acquires an α-helical structure in presence of TFE.
Protein: DP03623 (UniProt P0DTC1)
Region: residues 4393	to 4405
Annotation: lipid binding (Molecular function)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Analogous to lipid membranes, the SDS micelles used to mimic the interface between hydrophobic and hydrophilic environments such as the plasma membrane and the cytosol [34]. SDS is a denaturing detergent with folding inducing properties that form micelles (CMC is 1.99 mM in 50 mM phosphate buffer [35])
At higher concentrations (25, 50, and 100 mM) the CD spectra of nsp11 exhibited two minima at 206 and 222 nm suggesting the structural transition from the disordered to ordered conformation (Fig. 3A and B).
Protein: DP03624 (UniProt Q6ZMT4)
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 disordered residues include the C-terminal tail (residues 480–488) and the N-
terminal tail (residues 1–31), the latter of which is absent in the KIAA1718 orthologs of zebrafish and Xenopus laevis (Supplementary Fig. 2) and whose deletion has no impact on activity (Supplementary Fig. 6).
(c) KIAA1718 contains four segments: a disordered alanine-rich sequence followed by a stretch of prolines, a PHD domain (blue) containing two zinc metals (gray balls), a rigid linker (cyan) and a jumonji domain (green) followed by a four-helix bundle.
Cross-references: PDB:3KV6
PDB:3KV5
Protein: DP03625 (UniProt Q5NCY0)
Region: residues 1132	to 1156
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The free-form crystals of JmjD3 were produced with construct 1132-1641. Since the 1132-1156 segment was disordered in the free JmjD3 structure, a truncated 1157-1641 construct was inserted into the same vector.
Despite numerous attempts at co-crystallization of mouse JmjD3 with H3K27me3 peptide, we failed to observe density for the peptide in the crystal structure of the complex. In order to get the peptide-bound JmjD3 structure, we used the engineered mouse JmjD3(1157-1641)-H3 construct described above, in which a PreScission protease site, H3(24-34) and a short linker replaced a disordered internal loop spanning amino acids 1293-1323.
Protein: DP03625 (UniProt Q5NCY0)
Region: residues 1293	to 1323
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
This truncated JMJD3 protein encompasses residues 1,157 to 1,641 and includes a cleaved insertion segment that replaces a disordered loop, to facilitate crystal packing and peptide binding (Supplementary Fig. 2a, b).
In this construct, a peptide segment containing a protease cleavage, H3 peptide and linker, replaced a disordered loop segment, with subsequent cleavage at the protease site.
The gene coding for peptide sequence LEVLFQGP-TKAARKSAPATGG-GSSGS (corresponding to PreScission protease site, histone H3(22-34) and a short linker)
was inserted and replaced a structurally disordered coding segment 1293-1323, with this construct designated as engineered mouse JmjD3(1157-1641)
Despite numerous attempts at co-crystallization of mouse JmjD3 with H3K27me3 peptide, we failed to observe density for the peptide in the crystal structure of the complex. In order to get the peptide-bound JmjD3 structure, we used the engineered mouse JmjD3(1157-1641)-H3 construct described above, in which a PreScission protease site, H3(24-34) and a short linker replaced a disordered internal loop spanning amino acids 1293-1323.
Protein: DP03626 (UniProt O15054)
Region: residues 1141	to 1176
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Even if the authors didn't specify the disorder state of the region 1141-1176 as well as they described for mouse JmjD3/KDM6B in the same reference, this segment is absent in PDB
Cross-references: PDB:4ASK
PDB:2XUE
Protein: DP03626 (UniProt O15054)
Region: residues 1293	to 1322
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Even if the authors didn't specify the disorder state of the loop 1292-1322 as well as they described for mouse JmjD3/KDM6B in the same reference, this segment is absent in PDB
Cross-references: PDB:4ASK
PDB:2XUE
Protein: DP03626 (UniProt O15054)
Region: residues 1141	to 1157
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Even if the authors didn't specify the disorder state of the region 1141-1157, this segment is absent in PDB
Cross-references: PDB:5OY3
Protein: DP03626 (UniProt O15054)
Region: residues 1292	to 1323
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Even if the authors didn't specify the disorder state of the region 1292-1323, this segment is absent in PDB
Cross-references: PDB:5OY3
Protein: DP03627 (UniProt O15550)
Region: residues 1048	to 1077
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The helical domain, the linker region, the jumonji domain, and the zinc-binding domain are colored pink, orange, blue, and green, respectively. Disordered regions are shown with dashed lines.
Cross-references: PDB:3AVR
PDB:3AVS
Protein: DP03627 (UniProt O15550)
Region: residues 1051	to 1077
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Even if the authors didn't specify as disordered the region 1051-1077, these residues are absent in PDB
Cross-references: PDB:6FUL
PDB:6FUK
Protein: DP03628 (UniProt P52732)
Region: residues 1	to 15
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1–15, 271–279, and 366 –368 in the first monomer and residues 1–15, 271–284, and 366 –368 in the second were not observed in the electron density.
Cross-references: PDB:1II6
Protein: DP03628 (UniProt P52732)
Region: residues 1	to 16
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The authors didn't specify the state of the first 16 residues in the first and second monomer, but these residues were not observed in the PDB
Cross-references: PDB:2FME
Protein: DP03628 (UniProt P52732)
Region: residues 272	to 286
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 55–58 (L2) and 272–286 (L11) are missing for molecules A and B (Figure 2A). These loop regions are also missing in other Eg5 structures.
Residues 55–60 (L2) and 272–286 (L11) are missing for molecules A and B.
The dotted lines indicate the disordered regions.
Cross-references: PDB:5ZO7
PDB:5ZO9
PDB:5ZO8
Protein: DP03628 (UniProt P52732)
Region: residues 272	to 286
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the former space group, loops containing residues 56–60, 176–179, 249-243 and 272–286 are missing in the structure, whereas in the latter space group the regions 34–35 and 272–287 are absent.
Cross-references: PDB:6G6Z
PDB:6G6Y
Protein: DP03628 (UniProt P52732)
Region: residues 108	to 126
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Four regions corresponding to residues 57–58 (L2), 108–126 (regions of the P-loop, N-terminal α2, and L5), 225–231 (L9), and 270–287 (L11) are missing due to high flexibility (Figure 2A). The large flexible loop, L5, which is typically inserted in the middle of the α2 helix in other Eg5 structures, is absent in Eg5-PVZB1194 (Supporting Information, Figure S1). 
Dotted lines indicate the disordered regions. 
The ATP-binding pocket mainly consists of P-loop, L9, and L11, which is surrounded by α1, β3, α2, and L5. In the structure of Eg5-PVZB1194, residues Thr107 and Glu129, instead of a nucleotide, occupy the ATP-binding site of Eg5-AMPPNP, although residues 108–126 are disordered (Figure 5A)
Cross-references: PDB:3WPN
Protein: DP03628 (UniProt P52732)
Region: residues 270	to 287
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Four regions corresponding to residues 57–58 (L2), 108–126 (regions of the P-loop, N-terminal α2, and L5), 225–231 (L9), and 270–287 (L11) are missing due to high flexibility (Figure 2A). The large flexible loop, L5, which is typically inserted in the middle of the α2 helix in other Eg5 structures, is absent in Eg5-PVZB1194 (Supporting Information, Figure S1). 
Dotted lines indicate the disordered regions. 
The charged amino acids in L11, missing in the crystal structure due to its high flexibility, are located close to the entrance of the biphenyl-binding pocket (Figure 2A). 
Cross-references: PDB:3WPN