LiteFold/DisProt huggingface dataset:
Protein: DP03596 (UniProt P25368)
Region: residues 106	to 119
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
N-terminal residues 1–80 of Utp22, C-terminal residues 190–297 of Rrp7, and several internal loops of each protein were not visible in the crystal structure, likely due to structural flexibility. SDS-PAGE analysis of dissolved crystals showed that Utp22 was intact and Rrp7 was partially degraded (unpublished data).
In addition, two prominent tentacle-like structures project from the NTD to reach the more distant D6 of Utp22. One tentacle comprises a long loop between strands b4 and b5. This loop is disordered in the C-terminal half and its sequence is highly variable among Rrp7 orthologs (Figure 2B and Text S2).
The current model contains Utp22 residues 81–274, 282–317, 326–445, 453–983, 1010 1116, and 1128–1237; Rrp7 residues 3–27, 32–105, and 120–189; 764 water molecules; 11 sulfate ions; and three PEG molecules.
Cross-references: PDB:4M5D
Protein: DP03597 (UniProt P02994)
Region: residues 442	to 458
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 2–441 in eEF1A and 117–206 in eEF1Bα were modeled, while amino acids 1 and 442–452 in eEF1A and 110–116 in eEF1Bα are disordered. 
Residues 442-458 are disordered in the structure.
Cross-references: PDB:1F60
Protein: DP03597 (UniProt P02994)
Region: residues 454	to 458
Annotation: methylation display site (Disorder function)
Evidence: in vitro demethylation assay evidence used in manual assertion
Supporting statements:
Because the base-labile, volatile [methyl-3H]radioactivity of eEF1A could be released by trypsin treatment but not by carboxypeptidase Y or chymotrypsin treatment, we suggest that the methyl ester is present on the α-carboxyl group of its C-terminal lysine residue.
The rapid turnover of the methyl ester suggests that the methylation/demethylation of eEF1A at the C-terminal carboxyl group may represent a novel mode of regulation of the activity of this protein in yeast.
However, the existence of the C-terminal carboxyl methyl ester identified in this study has not been previously recognized.
Significantly, we found that [3H]methanol was released when the 49-kDa polypeptide was digested by trypsin but that little or no [3H]methanol was released with CPY, chymotrypsin, or buffer alone (Fig. 5A). The C-terminal amino acid residue of yeast eEF1A is lysine (15). Therefore, trypsin would be expected to cleave C-terminally to this residue and, if it is methyl esterified, release methanol (28, 29). Chymotrypsin, with its specificity for aromatic residues, would not be expected to cleave this linkage.
Thus, the data from the in vivo experiments shown in Fig. 5 are consistent with the data from the control experiments from Table I and indicate that the methyl ester on the eEF1A C-terminal lysine residue can be hydrolyzed by trypsin but not by CPY and chymotrypsin. The inability of CPY to cleave the lysine α-carboxyl methyl ester under these conditions may reflect the effect of the positively charged side chain. Taken together, these results indicate that the methyl ester linkage on eEF1A is on the carboxyl group of its C-terminal lysine residue.
We set out to identify novel methylesterified proteins in yeast and identified a major methylated polypeptide as eEF1A that is not only amino-methylated on some internal lysine residues but is also carboxyl methylated at the C terminus.
Protein: DP03598 (UniProt Q6VRZ6)
Region: residues 101	to 137
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The protein adopts an eight-stranded β-barrel conformation, which encompasses amino acids 151-255, whereas the remaining residues include a short α-helix (138-141) and a flexible tail (101-137), which probably serves as a linker to the N-terminal A region of the protein.
The structure consists of an eight-stranded antiparallel β-barrel overlaid by a short α-helix with an unstructured N-terminal end.
The rest of the molecule (101-137) is characterized by a low number of long range NOEs, which determine higher RMSD values (Fig. 2).
Cross-references: PDB:1YS5
BMRB:16058
Protein: DP03599 (UniProt Q9JYK4)
Region: residues 470	to 546
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-lobe of NmLbpB is composed of residues 359–718 and found largely disordered in the crystal structure as evident from higher B-factors for this region compared to the rest of the structure (Figure 3C).
The C-lobe of NmLbpB hashigh B-factors with the large loops of this lobe not observed in our structure; the black arrow indicates the putative location of these loops.
Cross-references: PDB:7JRD
Protein: DP03600 (UniProt Q9JXV4)
Region: residues 20	to 46
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The protein N-terminus (66-92) is missing from the pdb structure.
Cross-references: PDB:7LCV
Protein: DP03600 (UniProt Q9JXV4)
Region: residues 23	to 48
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The protein N-terminus (69-94) is missing from the pdb structure.
Cross-references: PDB:5T5F
Protein: DP03600 (UniProt Q9JXV4)
Region: residues 23	to 33
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The protein N-terminus (69-79) is missing from the pdb structure.
Cross-references: PDB:2YPV
Protein: DP03600 (UniProt Q9JXV4)
Region: residues 34	to 48
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The region is folded in the pdb but not mentioned in the article.
Cross-references: PDB:2YPV
Protein: DP03600 (UniProt Q9JXV4)
Region: residues 34	to 48
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The region is folded in the pdb but was disordered in absence of the antibody.
Cross-references: PDB:2YPV
Protein: DP03601 (UniProt Q9JXP1)
Region: residues 501	to 516
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the course of monitoring the LtgA reaction in the crystalline state, we captured a native version of LtgA with a distinctly disordered alpha helix 30 (Figure 1a–b, Video 1).
Cross-references: PDB:6H5F
Protein: DP03601 (UniProt Q9JXP1)
Region: residues 1	to 40
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-t is missing from the structure.
Cross-references: PDB:6H5F
Protein: DP03601 (UniProt Q9JXP1)
Region: residues 501	to 516
Annotation: order to disorder (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
In the course of monitoring the LtgA reaction in the crystalline state, we captured a native version of LtgA with a distinctly disordered alpha helix 30 (Figure 1a–b, Video 1). This represents a newly identified conformational state of LtgA whereby alpha helix 30 transitions from an ordered to a disordered state (Figure 1a–b).
Cross-references: PDB:6H5F
Protein: DP03601 (UniProt Q9JXP1)
Region: residues 501	to 516
Annotation: catalytic activity (Molecular function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
LtgA is involved in maintaining the structural composition of the peptidoglycan
However, the PG of the ΔltgAltgAΔ30 strain was found to be markedly hyperacetylated when compared to that of the other strains, with a 102% increase in the amount of acetylated GlcNAc-anhMurNAc-tetrapeptide (GM*4), a 39% increase in acetylated GlcNAc-anhMurNAc-tetrapeptide crosslinked with GlcNAc-MurNAc-tetrapeptide (GM*4-GM4), and a 46% increase in doubly acetylated di-GlcNAc-anhMurNAc-tetrapeptide (GM*4 GM*4) (Figure 4, Figure 4b).
Protein: DP03601 (UniProt Q9JXP1)
Region: residues 501	to 516
Annotation: order (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The architecture of the active site of LtgA is formed by a total of 10 α-helices (α28, α29, α30, α31, α32, α33, α34, α35, α36, and α37; Fig. S2, a–d). A six-helix bundle (α29, α30, α31, α32, α33, and α34) constitutes the active site core, which secures the glycan chain.
Cross-references: PDB:6FPN
PDB:5O2N
PDB:5O24
PDB:5O29
PDB:5O1J
Protein: DP03604 (UniProt Q93EK7)
Region: residues 283	to 311
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The protein C-t is missing from the pdb structure.
Cross-references: PDB:1SS9
Protein: DP03604 (UniProt Q93EK7)
Region: residues 283	to 311
Annotation: flexible C-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The protein C-t is missing from the pdb structure.
Cross-references: PDB:1SS9
Protein: DP03605 (UniProt Q9JZ55)
Region: residues 238	to 250
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
As in the wild-type structure, loops β7α7 and β8α8 are disordered, showing noncontinuous electron density.
Cross-references: PDB:3QPY
PDB:3QQ0
PDB:3QQ1
PDB:3QPZ
Protein: DP03605 (UniProt Q9JZ55)
Region: residues 240	to 250
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The β8-α8 loop (240-250) is missing from the pdb structures due to its flexibility.
Cross-references: PDB:4JTL
PDB:4JTF
PDB:4JTE
PDB:4JTK
PDB:4JTI
PDB:4JTJ
PDB:4JTG
Protein: DP03606 (UniProt P0CE18)
Region: residues 20	to 99
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Since the threefold axes of the THCC and NTD are not collinear with the threefold axis of a CTD, this naturally leads to disorder in the THCC and the portion of the NTD that does not directly interact with the CTD via crystal packing. 
The PDB’s validation RSRZ score corroborates the disorder observed in residues 20–99. The disorder becomes a progressive effect when moving away from the interface of the CTD and NTD.
Cross-references: PDB:6GJT
Protein: DP03606 (UniProt P0CE18)
Region: residues 91	to 99
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Since the threefold axes of the THCC and NTD are not collinear with the threefold axis of a CTD, this naturally leads to disorder in the THCC and the portion of the NTD that does not directly interact with the CTD via crystal packing. 
The PDB’s validation RSRZ score corroborates the disorder observed in residues 20–99. The disorder becomes a progressive effect when moving away from the interface of the CTD and NTD.
THCC connecting NTD and CTD.
Protein: DP03607 (UniProt Q9K169)
Region: residues 1	to 14
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In all structures, no electron density for the 14 amino acids at the N-terminus of each NmeDAH7PS chain could be found, which is attributed to these residues being part of a conformationally highly flexible allosteric binding loop [17].
Cross-references: PDB:4UMB
PDB:4UMC
PDB:4UMA
Protein: DP03607 (UniProt Q9K169)
Region: residues 1	to 14
Annotation: flexible N-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In all structures, no electron density for the 14 amino acids at the N-terminus of each NmeDAH7PS chain could be found, which is attributed to these residues being part of a conformationally highly flexible allosteric binding loop [17].
Cross-references: PDB:4UMA
PDB:4UMC
PDB:4UMB
Protein: DP03608 (UniProt A6YID9)
Region: residues 1	to 38
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure of CsStefin-1 was determined in amino acid residues 39–136 because the electron density for residues 28–38 on the loop region was poor.
Cross-references: PDB:5ZC1
Protein: DP03609 (UniProt H2L2M0)
Region: residues 91	to 117
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the crystal structure of Na-SLP-1, the C-terminal extension of about 30 amino acids, which is attached to the N-terminal Sap domain could not be resolved, which agrees with the results from mass spectrometry.
Cross-references: PDB:3S63
Protein: DP03609 (UniProt H2L2M0)
Region: residues 91	to 117
Annotation: disorder (Structural state)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
Mass spectrometry of Na-SLP-1 indicates that the protein degrades over time, whereas Ac-SLP-1 remains intact (9531 g/mol; theoretical M = 9531 g/mol).
Protein: DP03610 (UniProt O76744)
Region: residues 1	to 23
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Disordered region comprising the protein signal peptide.
Cross-references: PDB:3NT8
Protein: DP03611 (UniProt Q9JZN9)
Region: residues 267	to 323
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, soaking the rigid cadmium-bound conformation of ZnuD with free zinc increased the dynamic flexibility of the protruding loops on interaction with its metal substrate and furthermore identified a potential periplasmic zinc-binding site (Fig. 2c and Supplementary Fig. 5).
Together, resolution of three unique receptor intermediates illustrates the ability of ZnuD to capture its substrate using multiple binding sites on flexible loops and, ultimately, drag zinc ions towards a buried high-affinity binding site.
Cross-references: PDB:4RVW
Protein: DP03611 (UniProt Q9JZN9)
Region: residues 267	to 323
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
On the other hand, soaking the rigid cadmium-bound conformation of ZnuD with free zinc increased the dynamic flexibility of the protruding loops on interaction with its metal substrate and furthermore identified a potential periplasmic zinc-binding site (Fig. 2c and Supplementary Fig. 5).
Together, resolution of three unique receptor intermediates illustrates the ability of ZnuD to capture its substrate using multiple binding sites on flexible loops and, ultimately, drag zinc ions towards a buried high-affinity binding site.
The presence of zinc modulates the dynamic flexibility of the external loops by remodelling an α-helical segment into a pair of β-strand motifs (Fig. 2a,b).
Cross-references: PDB:4RDR
Protein: DP03611 (UniProt Q9JZN9)
Region: residues 458	to 480
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, soaking the rigid cadmium-bound conformation of ZnuD with free zinc increased the dynamic flexibility of the protruding loops on interaction with its metal substrate and furthermore identified a potential periplasmic zinc-binding site (Fig. 2c and Supplementary Fig. 5).
Together, resolution of three unique receptor intermediates illustrates the ability of ZnuD to capture its substrate using multiple binding sites on flexible loops and, ultimately, drag zinc ions towards a buried high-affinity binding site.
The presence of zinc modulates the dynamic flexibility of the external loops by remodelling an α-helical segment into a pair of β-strand motifs (Fig. 2a,b).
Cross-references: PDB:4RVW
Protein: DP03611 (UniProt Q9JZN9)
Region: residues 458	to 480
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
On the other hand, soaking the rigid cadmium-bound conformation of ZnuD with free zinc increased the dynamic flexibility of the protruding loops on interaction with its metal substrate and furthermore identified a potential periplasmic zinc-binding site (Fig. 2c and Supplementary Fig. 5).
Together, resolution of three unique receptor intermediates illustrates the ability of ZnuD to capture its substrate using multiple binding sites on flexible loops and, ultimately, drag zinc ions towards a buried high-affinity binding site.
The presence of zinc modulates the dynamic flexibility of the external loops by remodelling an α-helical segment into a pair of β-strand motifs (Fig. 2a,b).
Cross-references: PDB:4RDR
Protein: DP03611 (UniProt Q9JZN9)
Region: residues 635	to 651
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, soaking the rigid cadmium-bound conformation of ZnuD with free zinc increased the dynamic flexibility of the protruding loops on interaction with its metal substrate and furthermore identified a potential periplasmic zinc-binding site (Fig. 2c and Supplementary Fig. 5).
Together, resolution of three unique receptor intermediates illustrates the ability of ZnuD to capture its substrate using multiple binding sites on flexible loops and, ultimately, drag zinc ions towards a buried high-affinity binding site.
The presence of zinc modulates the dynamic flexibility of the external loops by remodelling an α-helical segment into a pair of β-strand motifs (Fig. 2a,b).
Cross-references: PDB:4RVW
Protein: DP03611 (UniProt Q9JZN9)
Region: residues 635	to 651
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
On the other hand, soaking the rigid cadmium-bound conformation of ZnuD with free zinc increased the dynamic flexibility of the protruding loops on interaction with its metal substrate and furthermore identified a potential periplasmic zinc-binding site (Fig. 2c and Supplementary Fig. 5).
Together, resolution of three unique receptor intermediates illustrates the ability of ZnuD to capture its substrate using multiple binding sites on flexible loops and, ultimately, drag zinc ions towards a buried high-affinity binding site.
The presence of zinc modulates the dynamic flexibility of the external loops by remodelling an α-helical segment into a pair of β-strand motifs (Fig. 2a,b).
Cross-references: PDB:4RDR
Protein: DP03611 (UniProt Q9JZN9)
Region: residues 25	to 41
Annotation: disorder (Structural state)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The N-t domain is disordered in the crystal structure.
Cross-references: PDB:4RDR
PDB:4RVW
PDB:4RDT
Protein: DP03611 (UniProt Q9JZN9)
Region: residues 265	to 275
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Cluster #1 (241-HSHEYDDCHAD-251, coloured green) contains two cadmium-binding sites identified within the cadmium co-crystal structure of ZnuD.
Cross-references: PDB:4RDR
Protein: DP03611 (UniProt Q9JZN9)
Region: residues 312	to 322
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Snapshots from Supplementary Movie 1 illustrate the putative flexibility of the extracellular loop 3 during the MD simulations of ZnuD in lipid bilayer in the absence (a) and presence (b) of 100 mM ZnCl2. The extracellular loop 3 contains two clusters (coloured pink and green) previously suggested as putative zinc-binding sites13 due to the high percentage of histidine, aspartic and glutamic acid residues situated there (drawn in stick representation).
Cross-references: PDB:4RDR
Protein: DP03612 (UniProt J9ULM6)
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:
Region corresponding to the signal peptide of the protein and unstructured in the crystal structure, as mentioned in Table 1.
Cross-references: PDB:4NUN
PDB:4NUO
PDB:4NUI
PDB:4NUK
Protein: DP03613 (UniProt P46434)
Region: residues 11	to 33
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The OvGST1 shows an N-terminal 25-amino-acid extension before sequence identity to other σ-class GSTs begins. The extension is not ordered and therefore not defined by the electron density; however, the crystal packing allows enough space to accommodate the extension within the gaps.
Cross-references: PDB:2HNL
Protein: DP03614 (UniProt Q7DDR9)
Region: residues 59	to 73
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region is missing in the crystal structure.
Cross-references: PDB:5CGL
Protein: DP03614 (UniProt Q7DDR9)
Region: residues 178	to 191
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Autoadenylylation of NmFic was monitored in real-time by circular dichroism (CD) spectroscopy. Because NmFicwt shows little autoadenylylation (Fig. 3B), we used NmFicmono (NmFicE102R,E156R) for this and the following analyses. Upon addition of ATP/MgCl2, the CD spectrum of NmFicmono showed a gradual, time-dependent decrease in amplitude of the negative peaks at 208 and 222 nm (Fig. S5A), corresponding to a reduction of α-helical content. This decrease is entirely consistent with (partial) unfolding of the αinh upon autoadenylylation.
Protein: DP03614 (UniProt Q7DDR9)
Region: residues 178	to 191
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
αinh of Autoadenylylated NmFic Is Partly Unfolded.
We obtained well-dispersed NMR spectra for an unmodified protein (catalytically inactive NmFicmono,H107A), as well as for autoadenylylated (NmFicmono-AMP) protein.
Furthermore, the amide chemical shifts of residues 178–191 populate the random coil region (7.5–8.5 ppm), indicating an unfolded conformation.
Cross-references: BMRB:26607