LiteFold/DisProt huggingface dataset:
Protein: DP03261 (UniProt P75966)
Region: residues 1	to 36
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystals of the full-length enzyme contain two molecules in the asymmetric unit and in both molecules the N-terminal domain is disordered.
Density for the N-terminal 35 amino acids of RluE was not visible in electron density maps calculated for either truncated or full-length RluE. A large single crystal of fulllength RluE was carefully washed in protein-free mother liquor, dissolved in water and run on an SDS-PAGE gel in order to find out if full-length RluE had undergone proteolysis during crystallization. The gel showed a single protein band with the molecular mass of full-length RluE. Therefore, the N-terminal 35 residues of RluE must be disordered in the crystal.
The disordered N-terminal residues may comprise a separate protein domain that vibrates as a rigid body. Other Ψ synthases in the RsuA family contain an S4-like domain at their N-termini that is postulated to bind nonspecifically to RNA substrate29; 30.
The RNA-binding domains of Ψ synthases are usually attached to the rest of the protein by a flexible tether, and so are frequently disordered in crystal structures of the apo enzymes. The N-terminal 35 residues of E. coli RluE contain six arginines and three lysines. The basic nature of the N-terminal region is consistent with its putative role in RNA binding.
For the truncated protein structure, rounds of rebuilding and addition of solvent molecules using Quanta (Accelrys, San Diego, CA), alternated with restrained refinement of atomic positions and isotropic temperature factors in CNS42 were carried out until the R-factor reached 20.1% (Rfree=21.3%). There was no electron density for residues before Asn-36 or for residue Glu-159 in loop L7–8 (Fig. 1); these residues are either not present in the truncated protein or are disordered in the crystals. An analysis of the geometry45 shows that all refinement statistics are well within the expected values at this resolution (Table 2).
Full-length RluE was refined in a similar manner, except that anisotropic B-factors were not refined, and only CNS and REFMAC5 were used for refinement. The two protein molecules in the asymmetric unit had slightly different conformations, so non-crystallographic symmetry restraints were not used. No density for residues 1–37 in one molecule or 1–38 in the other was present in electron density maps, and Glu-159 was also disordered in both molecules.
Cross-references: PDB:2OLW
Protein: DP03262 (UniProt P01009)
Region: residues 26	to 47
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
22 N-terminal amino acids and the histidine tag were not visible in the final electron density maps
The structure defined in this paper comprises residues 26-418
The IDR characterized in the publication and spanning the N-terminal residues of the crystal structure corresponds to region 26-47 of the amino acid sequence, since the natural precursor form of the protein contains a signal peptide (1-24) that is cleaved in the mature secreted protein.
Cross-references: PDB:1OO8
Protein: DP03262 (UniProt P01009)
Region: residues 25	to 42
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The  first 18 residues were not visible in the electron density map.
The structure defined in this paper comprises residues 25-418
he IDR characterized in the publication and spanning the N-terminal residues of the crystal structure corresponds to region 25-42 of the amino acid sequence, since the natural precursor form of the protein contains a signal peptide (1-24) that is cleaved in the mature secreted protein.
Cross-references: PDB:1HP7
Protein: DP03262 (UniProt P01009)
Region: residues 25	to 43
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The missing residues  are the N-terminal 19 residues, which are also missing in the starting model
The structure defined in this paper comprises residue 25-418
The IDR characterized in the publication and spanning the N-terminal residues of the crystal structure corresponds to region 25-43 of the amino acid sequence, since the natural precursor form of the protein contains a signal peptide (1-24) that is cleaved in the mature secreted protein.
Cross-references: PDB:1KCT
Protein: DP03263 (UniProt O80358)
Region: residues 86	to 102
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model, comprising residues 2 to 86, 101 to 261 and 268 to 286, was refined to an Rfree of 0.219 and RWork of 0.210 at 1.7 Å resolution.
From the description of the final model, it can be inferred that there is a disorder region from positions 87 to 100, however the region of missing residues in the pdb is from 86 to 102.
Cross-references: PDB:3TWL
PDB:3TWM
PDB:3TWK
Protein: DP03265 (UniProt O48963)
Region: residues 581	to 592
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the AtLOV2 structure the disordered residues 581–592 of the junction
in chain A and the partially ordered residues 580–586 in chain B
presumably adopt a loop conformation
Cross-references: PDB:4HHD
Protein: DP03266 (UniProt Q9M658)
Region: residues 1700	to 1728
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 1700 to 1728 and 1811 to 1814 are
disordered or very poorly ordered in every CMM2 molecules. 
Cross-references: PDB:3VEM
Protein: DP03267 (UniProt Q9FIC3)
Region: residues 75	to 84
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The disordered region was not stated in the paper, but observed in the PDB structure (2MM9). It spans from the end of the sheet beta-3' to the beginning of helix alpha-4.
Protein: DP03268 (UniProt Q682I1)
Region: residues 96	to 108
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
All secondary structures are connected by short loops (1–4
residues) except the one situated between beta-1 and beta-2. This
beta1-beta2 loop that we refer to as [H/C] loop contains the histidine
and cysteine residues from BolA_H and BolA_C groups,
respectively. In accordance with the existence of two groups,
the [H/C] loop can be formed by 11+/-6 (up to 20) residues in
BolA_H members
Start and end position of the H/C were taken from PDB 4PUG.
Cross-references: PDB:4PUG
Protein: DP03269 (UniProt Q9C552)
Region: residues 258	to 270
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
A remarkable feature of the structure of APUM2385-655 is the unique characteristics of R3.
This PUF repeat contains 74 amino acid residues (residues
213–286) and includes an insertion (residues 235–270; the
electron density of residues 258–270 was missing) located
between the second and third helix. The insertion comprises
a disordered region and two short -helices (i1 and i2),
located at the inner concave surface, that participate in the
recognition of RNA bases
Cross-references: PDB:5WZI
PDB:5WZH
PDB:5WZG
PDB:5WZK
PDB:5WZJ
Protein: DP03269 (UniProt Q9C552)
Region: residues 258	to 270
Annotation: RNA binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
A remarkable feature of the structure of APUM2385-655 is the unique characteristics of R3.
This PUF repeat contains 74 amino acid residues (residues
213–286) and includes an insertion (residues 235–270; the
electron density of residues 258–270 was missing) located
between the second and third helix. The insertion comprises
a disordered region and two short -helices (i1 and i2),
located at the inner concave surface, that participate in the
recognition of RNA bases
Cross-references: PDB:5WZI
PDB:5WZH
PDB:5WZG
PDB:5WZK
PDB:5WZJ
Protein: DP03270 (UniProt Q00958)
Region: residues 396	to 420
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Figure 2 Sequence alignments. (A) Aligned C-terminal amino-acid sequences of LFY (Arabidopsis thaliana, AAA32826), BgLFY (Brownea
grandiceps, AAS79888), FLO (Antirrhinum majus, P23915), NymodLFY (Nymphea odorata, AAF77609), WelLFY (Welwitschia mirabilis,
AAF23870), MatstLFY (Matteuccia struthiopteris, AAF77608) and PpLFY1 (Physcomitrella patens, BAD91043). Identical and conservatively substituted residues are depicted on a grey ackground. Secondary structure elements are indicated. Residues involved in interactions with DNA bases and backbone are labelled with red and blue circles, respectively. Dashed bars indicate isordered regions in the crystal, blue rectangles indicate the residues involved in dimerization. Green triangles indicate the position of Arabidopsis mutations and residues divergent in PpLFY1 are highlighted in pink. (B) Two DNA duplexes containing the LEAFY-binding sites from AP1 and AG promoters present in the LEAFY–DNA complex crystals are depicted. Base pairs related by a dyad (indicated by a black dot) are highlighted in yellow.
Figure 2 shows an alignment of LFY homologos. Positions 400 to 424 of LFY_ARATH are indicated as disoreded in the crystal, but positions numbers in the paper and the PDB do not correspond with Uniprot sequence. The corrected position numbers of the disordered region are 396 to 420.
Cross-references: PDB:2VY2
PDB:2VY1
Protein: DP03271 (UniProt P21580)
Region: residues 150	to 160
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The β7–β8 loop itself is disordered in all available OTU structures but, like the disordered loops in the unliganded S1 ubiquitin-binding site, it may undergo conformational changes upon binding a cognate partner that are hindered by the I325N substitution.
Cross-references: PDB:5V3B
PDB:5V3P
Protein: DP03271 (UniProt P21580)
Region: residues 213	to 228
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The β7–β8 loop itself is disordered in all available OTU structures but, like the disordered loops in the unliganded S1 ubiquitin-binding site, it may undergo conformational changes upon binding a cognate partner that are hindered by the I325N substitution.
Cross-references: PDB:5V3B
PDB:5V3P
Protein: DP03271 (UniProt P21580)
Region: residues 152	to 161
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In A20, two loops (residues 152-160 and 212-228) in this distal binding site are disordered despite high sequence conservation, and hence surface analysis in this region is not meaningful.
Cross-references: PDB:2VFJ
Protein: DP03271 (UniProt P21580)
Region: residues 213	to 227
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In A20, two loops (residues 152-160 and 212-228) in this distal binding site are disordered despite high sequence conservation, and hence surface analysis in this region is not meaningful.
Cross-references: PDB:2VFJ
Protein: DP03271 (UniProt P21580)
Region: residues 213	to 228
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
No large conformational changes occur upon Ub binding. However, two unstructured loops in A20 apo are stabilised by Ub, forming helix α6’ and the β2’-β2” sheet (compare Extended Data Fig. 2j).
Cross-references: PDB:5LRX
Protein: DP03272 (UniProt Q6GQQ9)
Region: residues 88	to 129
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first crystallised Cez apo construct (residues 88-438) contained an N-terminal flexible extension of 41 residues that was removed in subsequent crystallisation attempts for Cez apo and complexes.
Electron density was not visible for the first 41 residues, which were removed from the construct for subsequent crystallisation attempts.
Protein: DP03272 (UniProt Q6GQQ9)
Region: residues 267	to 291
Annotation: disorder (Structural state)
Evidence: author statement used in manual assertion
Supporting statements:
To obtain crystals of Cez~Ub, the long, unstructured V-loop (residues 267-291) was replaced by the corresponding sequence in TRABID (Gln-Pro-Gly; QPG).
Protein: DP03273 (UniProt Q99835)
Region: residues 539	to 640
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The residues 539–644 were not observed in the cryo-EM map, suggesting high flexibility of this region.
Cross-references: PDB:6XBJ
PDB:6XBL
Protein: DP03274 (UniProt Q9Y4K0)
Region: residues 763	to 774
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Crystals of hLOXL2 (residues 318–774 with N455Q) were grown at 18 °C using the hanging-drop vapor-diffusion method.
The atomic model comprising residues 322–762 was built and refined to 2.4-Å resolution.
Cross-references: PDB:5ZE3
Protein: DP03275 (UniProt Q15276)
Region: residues 642	to 661
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region of residues visible in the GAT–Rabaptin5 complex crystal is represented with capital letters, and mobile residues are in lowercase letters.
Cross-references: PDB:1X79
Protein: DP03276 (UniProt Q96PU8)
Region: residues 205	to 214
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The five N-terminal and 10 C-terminal residues and segments 32–39 and 61–68 were disordered in the crystal.
Cross-references: PDB:4JVH
Protein: DP03277 (UniProt Q61001)
Region: residues 70	to 119
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 70–119—another insertion into the jelly-roll motif—are disordered in the a5LN–LEa1–2 structure. The disordered region contains four conserved cysteines, but otherwise its sequence is highly variable in the LN domain superfamily
Cross-references: PDB:2Y38
Protein: DP03278 (UniProt P18065)
Region: residues 312	to 325
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
C-BP-2 has a longer disordered loop I, and an extended C-terminal tail, which is unstructured and very mobile.
The last 14 residues, 276–289, are unstructured.
Another noticeable feature of the C-BP-2 sequence relative to other IGFBP C- domains is its 11–13 residue extended C-terminal tail (Figure 2(e)). The solution structure of C-BP-2 shows clearly that this extended C-terminal tail is unstructured (Figure 1(a)).
Residues in the C-terminal tail beyond Gln277 exhibit J(0.87ωH) >15 ps rad- 1 and thus have even greater flexibility.
A possible explanation for the anomalously higher R2 values and the failure in fitting the relaxation parameters is that the motions of the core of C-BP-2 cannot be described by a simple anisotropic tumbling model with a unique diffusion tensor. This is probably a consequence of the presence of a longer and very flexible C-terminal tail, together with a longer disordered loop compared to C-BP-6.
The IDR characterized in the publication and spanning residues 276-289 corresponds to region 312-325 of the amino acid sequence, since the natural precursor form of the protein contains a signal peptide (1-35).
Cross-references: PDB:2H7T
Protein: DP03279 (UniProt Q08188)
Region: residues 463	to 472
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the zymogen, one monomer has missing density for a flexible loop between residues 461 and 479, and the second monomer has missing density for residues 460–472. In the active enzyme, residues 460–480 are missing in both monomers.
Residues 462–471 form a flexible solvent-exposed loop that links the last α-helical segment of the catalytic core domain to the first β-strand of the barrel 1 domain.
Residues 462-471 represent the minimal region where densities are missing in all monomers of  all X-ray structures of the protein. There is one residue shift between the paper and UniProt, due to cleavage of the initiator methionine.
Cross-references: PDB:1L9N
PDB:1L9M
Protein: DP03279 (UniProt Q08188)
Region: residues 463	to 472
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 462 to 471 form a highly flexible solventexposed loop that links the last alpha-helical segment of the catalytic core domain to the first beta-strand of the barrel 1 domain.
Both monomers have missing density for a flexible loop between residues 461–479.
Both monomers have missing density for a flexible loop between residues 462 and 478
Residues 462-471 represent the minimal region where densities are missing in all monomers of  all X-ray structures of the protein. Due to removal of the initiator methionine, there is one resiue shift between UniProt and the paper, Ser469 corresponds to UniProt residue 470.
Cross-references: PDB:1NUD
PDB:1NUF
PDB:1NUG
PDB:1L9M
Protein: DP03279 (UniProt Q08188)
Region: residues 468	to 472
Annotation: limited proteolysis display site (Disorder function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Residues 462-471 form a flexible solvent-exposed loop that link the last α-helical segment of the catalytic core domain to the first β-strand of the barrel 1 domain. This hinge region harbors Ser469, the cleavage site for proteolytic activation of the zymogen. This residue is flanked by polar residues, predicted to lie near the surface of the protein, which may be involved in recognition by an activating protease.
Due to removal of the initiator methionine, there is one resiue shift between UniProt and the paper, Ser469 corresponds to UniProt residue 470.
Protein: DP03279 (UniProt Q08188)
Region: residues 468	to 472
Annotation: limited proteolysis display site (Disorder function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
Proteolysis of the TGase 3 zymogen with dispase cleaves at Ser469 the flexible
hinge of sequences that joins the active site domain to beta-barrel 1 domains.
Due to removal of the initiator methionine, there is one resiue shift between UniProt and the paper, Ser469 corresponds to UniProt residue 470.
Protein: DP03280 (UniProt P19827)
Region: residues 653	to 672
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The construct-derived His6 tag and residues 35–44, 631–638, and 653–672 of HC1, which were clearly present in the protein preparation as determined by MS, were not visible in the electron density and are therefore assumed to be unstructured or highly conformationally labile.
Cross-references: PDB:6FPY
PDB:6FPZ
Protein: DP03280 (UniProt P19827)
Region: residues 35	to 44
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The construct-derived His6 tag and residues 35–44, 631–638, and 653–672 of HC1, which were clearly present in the protein preparation as determined by MS, were not visible in the electron density and are therefore assumed to be unstructured or highly conformationally labile.
Cross-references: PDB:6FPY
PDB:6FPZ
Protein: DP03280 (UniProt P19827)
Region: residues 653	to 657
Annotation: glycosylation display site (Disorder function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
In addition, the IRI heavy chains carried several O-linked glycans located on Thr619 of heavy chain 1 and a cluster of four O-linked oligosaccharides on Thr612, Ser619, Thr621, and Thr637 of heavy chain 2.
Edman degradation of the C-terminal HC1 peptide, Thr608-Arg627, identified Thr619 as the site of O-glycosylation.
Thus the carbohydrate attached to HC1 Thr619 is a trisaccharide composed of (Thr)-GalNAc-Gal-SA (Figure 2B).
In addition to the N-glycans, the IRI heavy chains also carry 5 O-linked trisaccharides: one attached to HC1 Thr619 and a cluster of four near the C-terminus of HC2 (Figure 3).
Thr619 corresponds to Thr653, since the natural precursor form of the protein contains a signal peptide (1-27) and a propeptide (28-34).
Protein: DP03280 (UniProt P19827)
Region: residues 668	to 672
Annotation: carbohydrate binding (Molecular function)
Evidence: mass spectrometry evidence used in manual assertion
Supporting statements:
As already pointed out by Enghild et al. [l], the C-terminal Asp residue, characterized by amino acid analysis of these peptides, was only identified with a low yield by Edman degradation. This is consistent with the fact that this residue is glycosylated.
Effectively fragment ions at mlz 679 for fraction 1 and mlz 652 for fraction 3 indicated that N-acetyl hexosamine is linked to the C-terminal Asp of each heavy chain.
A fragment ion at mlz 491 for fraction 3 (Fig. 6B) demonstrated that the linkage involves the C6 of the terminus (reducing) N-acetylhexosamine and the C-terminal Asp of H1.
The linkage to the H1 subunit involves an ester linkage between C6 of an internal N-acetylhexosamine and the C-terminal Asp638.
On the IT1 fragment obtained, two different tetrapeptides covalently linked to the chondroitin sulphate chain should be present: Val-Asp-ThrAsp proceeding from H1 and Val-Glu-Asn-Asp corresponding to the C-terminal sequence of H2.
Asp638 corresponds to Asp672, which is the C-terminal residue of the mature form of the protein, since the natural precursor form contains a signal peptide (1-27) and two propeptides (28-34 and 673-911).
Protein: DP03281 (UniProt Q2MKA7)
Region: residues 131	to 146
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Structure of (unbound) Rspo1-Fu1Fu2 (residues 31–145) at 2 Å resolution. Indicated are disulphide bonds (ball and stick) and disordered residues (dashed line).
Cross-references: PDB:4BSO