LiteFold/DisProt huggingface dataset:
Protein: DP03302 (UniProt G5EFZ1)
Region: residues 1	to 19
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model of iPGM-m consisted of two subunits with two Mn2 þ and Zn2 þ ions modelled within domain A of each subunit (Supplementary Fig. 9a) and the first 20 residues of the N terminus and last 13 residues of the C terminus were disordered and could not be modelled. The
two subunits are nearly identical with an RMSD deviation of 0.58 Å between Ca atoms for 517 residues aligned using GESAMT62 (Supplementary Fig. 9b). Crystals of the orthorhombic form (C. elegans iPGM-o) were obtained after approximately 6 months and diffracted to higher resolution than iPGM-m. Similarly, the N- and C-terminal residues were disordered in the iPGM-o as well.
From the apo iPGM structure we observed that the N-terminal
18 amino acids, unique to C. elegans iPGM, were disordered.
Cross-references: PDB:5KGM
PDB:5KGN
PDB:5KGL
Protein: DP03302 (UniProt G5EFZ1)
Region: residues 520	to 539
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model of iPGM-m consisted of two subunits with two Mn2 þ and Zn2 þ ions modelled within domain A of each subunit (Supplementary Fig. 9a) and the first 20 residues of the N terminus and last 13 residues of the C terminus were disordered and could not be modelled. The
two subunits are nearly identical with an RMSD deviation of 0.58 Å between Ca atoms for 517 residues aligned using GESAMT62 (Supplementary Fig. 9b). Crystals of the orthorhombic form (C. elegans iPGM-o) were obtained after approximately 6 months and diffracted to higher resolution than iPGM-m. Similarly, the N- and C-terminal residues were disordered in the iPGM-o as well.
Cross-references: PDB:5KGM
PDB:5KGN
PDB:5KGL
Protein: DP03303 (UniProt Q8IW75)
Region: residues 367	to 377
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The reactive center loop (RCL) (extending from G364 to P381) is flexible in the vaspin structure.
In one of the chains (A) of the 4IF8 structure the electron density is only missing for residues 367-377, not for the whole RCL.
Cross-references: PDB:4IF8
Protein: DP03303 (UniProt Q8IW75)
Region: residues 376	to 380
Annotation: limited proteolysis display site (Disorder function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
X-ray structures of SECs demonstrate that after initial cleavage of the RCL remaining residues beginning at the P15 glycine, following the standard nomenclature [28], are inserted into the β-sheet A as a new β-strand [27, 29].
SEC stands for serpin–enzyme complex (members of the serpin family typically form SDS-stable complexes with target proteases). 
UniProt explanation for this protease cleavage reaction: The reactive center loop (RCL) extends out from the body of the protein and directs binding to the target protease. The protease cleaves the serpin at the reactive site within the RCL, establishing a covalent linkage between the carboxyl group of the serpin reactive site and the serine hydroxyl of the protease. The resulting inactive serpin-protease complex is highly stable.
Cross-references: PDB:4IF8
Protein: DP03303 (UniProt Q8IW75)
Region: residues 367	to 377
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: mutant phenotype evidence used in manual assertion
Supporting statements:
It has been shown that the serpin inhibitory mechanism is critically dependent on the length of the RCL [31] and is furthermore structurally based on conserved small side-chain amino acids within the hinge region of inhibitory serpins. This also applies to vaspin, as the mutation of alanine 369 to proline (vaspinA369P) within the vaspin hinge region converts vaspin from inhibitor of hK7 to substrate.
The role of the Reactive Center Loop (RCL) in serpins is inhibition of proteases. I added the region 367-377 because that is the disordered fraction of the RCL.
Protein: DP03304 (UniProt P36952)
Region: residues 332	to 343
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The RCL loop in both monomers was observed to be mobile and relatively disordered and was not modeled fully in either monomer.
Cross-references: PDB:1XU8
PDB:1WZ9
Protein: DP03304 (UniProt P36952)
Region: residues 334	to 338
Annotation: limited proteolysis display site (Disorder function)
Evidence: enzymatic activity assay evidence used in manual assertion
Supporting statements:
Recombinant maspin (18 μm) was treated with 0.25 μm recombinant human cathepsin L (24) at 37 °C for 30 min in 0.1 m NaAc, pH 5.5, 1 mm EDTA, 0.1% Brij-35, 10 mm cysteine. Complete cleavage within the RCL was confirmed by SDS-PAGE, and the molecular masses of the cleaved products were found to be 38.24 and 4.707 kDa by mass spectrometry. Based on these data (and the observation that the only cysteine residue in the C-terminal peptide is buried and unmodified in all crystal structures) the position of the cleavage site was mapped to P5/P6 (SIE↓VPG).
The protease cleavage happens between residues 335 and 336 of the reactive center loop (RCL), which was annotated as regulation of limited proteolysis.
Protein: DP03305 (UniProt Q60675)
Region: residues 2730	to 2743
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 19 residues including the APLA sequence are disordered in the crystal.
The disordered portion of the N–terminus, which is unusual in that it contains many prolines and hydrophobic residues, is likely to interact with some part of LG1–LG3 in the complete laminin LG1–LG5 tandem.
Cross-references: PDB:1DYK
Protein: DP03306 (UniProt Q02297)
Region: residues 226	to 239
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The N- and C-terminal residues (1-2 and 50-63) and the Ω-loop comprising residues 24-30
are disordered. 
Comparison of the HRG-R EGF-like domain structure with the previously determined
structure of human EGF [Hommel et al. (1992) J. Mol. Biol. 227, 271-282] reveals a high degree of structural similarity; excluding the N-terminal region (residues 1-13), the disordered Ω-loop region (residues 24-30) that contains a three-residue insertion in HRG-R relative to hEGF, and the disordered C-terminal region (residues 50-63), the CR alignment between the HRG-R and hEGF minimized mean structures has a rms difference of ∼1 Å.
The C-terminal residues, Met51-Tyr63, are clearly disordered (Figures 4 and 5) and flexible (as judged from 15N relaxation measurements; W. J. Fairbrother, unpublished results) in solution.
Excluding the N-terminal region (Ser1-Phe13), the disordered Ω-loop (Lys24-Ser30), and the disordered Cterminal region (Pro50-Tyr63), the CR alignment between the HRG-R EGF-like domain and hEGF minimized mean structures is very good, with an rms difference of 0.98 Å
[this is likely within the accuracy limits of both structures (Zhao & Jardetzky, 1994)].
Pro20 and Tyr63 correspond to Pro226 and Tyr239
Cross-references: PDB:1HAF
PDB:1HAE
Protein: DP03306 (UniProt Q02297)
Region: residues 229	to 241
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The C-terminal flanking region outside the EGF-like domain (Val229-Lys241) is highly disordered and is not shown.
Cross-references: PDB:1HRE
PDB:1HRF
Protein: DP03307 (UniProt Q9UMD9)
Region: residues 2	to 455
Annotation: disorder (Structural state)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
The intracellular domain of BP180/collagen XVII is intrinsically disordered and partially folds in an anionic membrane lipid-mimicking environment.
The CD spectrum of BP180 ICD resembles one typical of a random coil structure (Fig. 3a), suggesting that bacterially expressed BP180 ICD is a disordered protein.
Protein: DP03307 (UniProt Q9UMD9)
Region: residues 2	to 455
Annotation: disorder to order (Structural transition)
Evidence: far-UV circular dichroism evidence used in manual assertion
Supporting statements:
Next, we measured the CD spectrum for BP180 ICD in the presence of negatively charged unilamellar DMPC:DMPG lipid vesicles with a 1:100 protein:lipid molar ratio. A clear change in the CD spectrum was seen (Fig. 3b), with a more pronounced negative CD signal at the 222 nm wavelength as well as a decrease in the negative peak at 198 nm. This indicates a partially α-helical conformation with some regions remaining disordered.
Protein: DP03307 (UniProt Q9UMD9)
Region: residues 2	to 455
Annotation: lipid binding (Molecular function)
Evidence: co-sedimentation assay evidence used in manual assertion
Supporting statements:
Therefore, we incubated His-BP180 ICD with and without DMPC-DMPG vesicles (1:100 protein:lipid molar ratio) and centrifuged sedimentable material. The majority of BP180 ICD was co-sedimented with DMPC-DMPG vesicles, while a small amount of protein stayed in the supernatant (Fig. 3c). Little aggregation and sedimentation of BP180 ICD was visible in the absence of lipid vesicles. These results confirm the binding of the BP180 ICD to negatively charged lipid vesicles.
Protein: DP03308 (UniProt Q96MS0)
Region: residues 654	to 667
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
We crystallized a complex of NELL2 EGF1–6 with Robo3 FN1, and Robo3 FN2–3 alone, following proteolysis within the 15-residue-long flexible linker between FN1 and FN2 in crystallization drops (Supplementary Fig. 2a)
Silver staining of the gels revealed that the first crystal form was likely NELL2 EGF1–6 complexed to Robo3 FN1 following proteolysis in the linker joining FN1 and FN2 domains (Supplementary Fig. 2a), and the second crystal form likely contained the remaining FN2 and FN3 domains of Robo3.
Protein: DP03308 (UniProt Q96MS0)
Region: residues 654	to 667
Annotation: flexible linker (Disorder function)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
We crystallized a complex of NELL2 EGF1–6 with Robo3 FN1, and Robo3 FN2–3 alone, following proteolysis within the 15-residue-long flexible linker between FN1 and FN2 in crystallization drops (Supplementary Fig. 2a)
Silver staining of the gels revealed that the first crystal form was likely NELL2 EGF1–6 complexed to Robo3 FN1 following proteolysis in the linker joining FN1 and FN2 domains (Supplementary Fig. 2a), and the second crystal form likely contained the remaining FN2 and FN3 domains of Robo3.
Protein: DP03309 (UniProt O60486)
Region: residues 642	to 659
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There is a large gap of ~30 Å between the end of the first rod and the beginning of the second (Fig. 2a). This gap is actually connected by the ~15-residue linker between the PSI2 and IPT2 domains (Supplementary Fig. 6), which is invisible in the cryo-EM map and therefore not included in the atomic model. 
Disorder is inferred from missing residues in the cryo-EM map. 
In contrast to class A plexins, the PSI2 and IPT2 domains in PlexinC1 are not rigidly connected to each other due to the flexible linker between them.
Cross-references: PDB:6VXK
Protein: DP03309 (UniProt O60486)
Region: residues 642	to 659
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
There is a large gap of ~30 Å between the end of the first rod and the beginning of the second (Fig. 2a). This gap is actually connected by the ~15-residue linker between the PSI2 and IPT2 domains (Supplementary Fig. 6), which is invisible in the cryo-EM map and therefore not included in the atomic model. 
Disorder is inferred from missing residues in the cryo-EM map. 
In contrast to class A plexins, the PSI2 and IPT2 domains in PlexinC1 are not rigidly connected to each other due to the flexible linker between them.
Cross-references: PDB:6VXK
Protein: DP03310 (UniProt Q3U4G3)
Region: residues 43	to 87
Annotation: disorder (Structural state)
Evidence: cleavage assay evidence used in manual assertion
Supporting statements:
Computational secondary structure analysis using PSIPRED (http://bioinf.cs.ucl.ac.uk/psipred/) predicted a largely unstructured loop at the N-terminus spanning ~S43–P95. We therefore subjected the purified protein to limited proteolysis by a panel of ten proteases (Proti-Ace &Proti-Ace 2 kit, Hampton Research). Based on the favorable cleavage pattern, we chose trypsin for preparative treatment with protein to trypsin ratio of 500:1 (w/w) and 4°C overnight incubation. The trypsinized sample was further purified by size-exclusion chromatography (Superdex 200, GE Healthcare) in 20 mM HEPES, pH 7.5, 150 mM NaCl. Mass spectrometry detected peptides from S87 to R373 in the purified sample, indicating a stable domain, which was subsequently shown to retain the enzyme activity.
The overall structure consists of ~300 residues (V93–E391), lacking the N-terminal unstructured loop (~S43–V92) that was removed by limited proteolysis (See Online Methods).
Protein: DP03311 (UniProt P00740)
Region: residues 47	to 93
Annotation: pre-molten globule (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
In the amide-amide proton region of the NOESY spectrum (Fig. 3), we observed sequential NH-NH contacts, which indicated α helical structure in the carboxyl terminus of the peptide(14). Following the assignment of all proton resonances, short range and medium range interactions were defined from the NOESY spectrum. The absence of any long range interactions indicated the lack of a compact tertiary structure or the presence of different conformers rapidly interconverting on an NMR time scale.
Of note, authors describe 3 structured regions, residues 6–9, 18–23, and 37–46. 
"These three structured segments exist autonomously in that they appear to have no interactions with each other or with other portions of the molecule (Fig. 6)."
The absence of any long range interactions indicated the lack of a compact tertiary structure or the presence of different conformers rapidly interconverting on an NMR time scale. 
The domain described by the authors corresponds to residues 47-93 of the UniProt sequence.
Cross-references: PDB:1CFH
Protein: DP03311 (UniProt P00740)
Region: residues 47	to 93
Annotation: pre-molten globule to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The domain described by the authors corresponds to residues 47-93 of the UniProt sequence.
Upon the addition of Ca(II), the proton spectrum revealed increased dispersion of resonances in all regions of the spectrum (>0.4 ppm from the random coil values) (Fig. 1B). Specifically, there were downfield-shifted amide proton resonances and upfield-shifted methyl proton resonances. In addition, the metal-free and Ca(II)-bound forms of the peptide were in slow exchange on an NMR time scale. For example, the tryptophan indole amide protons from apoFactor IX (1-47) and the Factor IX (1-47):Ca(II) binary complex could be observed simultaneously at 10.25 and 10.19 ppm, respectively. These results suggest that a new structure is adopted following the addition of calcium ions that is different from and likely more structured than the metal-free form.
Protein: DP03311 (UniProt P00740)
Region: residues 70	to 74
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 72 and 73 bind Ca+2 ions according to the crystal structure (PDB: 1NLO).
Protein: DP03311 (UniProt P00740)
Region: residues 47	to 93
Annotation: pre-molten globule to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The domain described by the authors corresponds to residues 47-93 of the UniProt sequence.
We now report the three-dimensional structure of
the Ca(II)-bound peptide in solution as determined by NMR
methods. A comparison of this structure with apo-factor IX
(1—47) reveals the nature of the Ca(ID-induced conformational transition in factor IX.
The tertiary structure consists of a large carboxyl-terminal
globular core (residues 13—47) adjacent to a large aminoterminal loop (residues 1-12) (Figure 6)
Cross-references: PDB:1CFI
Protein: DP03311 (UniProt P00740)
Region: residues 47	to 57
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The domain described by the authors corresponds to residues 47-93 of the UniProt sequence.
Upon occupancy of specific metal bindings sites that interact with many divalent cations, including Mg2+, the Gla domain assumes formal structure except that residues 1–11 remain flexible and motile. 
In contrast, the amino-terminal 11 residues lacked defined structure in Factor IX (1–47)-Mg2+, with the exception of a short loop from residue 6 to 9.
Cross-references: PDB:1MGX
Protein: DP03311 (UniProt P00740)
Region: residues 47	to 57
Annotation: disorder to order (Structural transition)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The domain described by the authors corresponds to residues 47-93 of the UniProt sequence.
With occupancy of another set of metal bindings, sites that can be occupied only by Ca2+, the entire polypeptide backbone of the Gla domain is defined, including the NH2-terminal loop (Fig. 5).
Protein: DP03311 (UniProt P00740)
Region: residues 70	to 74
Annotation: calcium ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 72 and 73 bind Ca+2 ions according to the crystal structure (PDB: 1NLO).
Cross-references: PDB:1NL0
Protein: DP03311 (UniProt P00740)
Region: residues 74	to 78
Annotation: calcium ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residue 76 binds Ca+2 ions according to the crystal structure (PDB: 1NLO).
Cross-references: PDB:1NL0
Protein: DP03311 (UniProt P00740)
Region: residues 74	to 78
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residue 76 binds Ca+2 ions according to the crystal structure (PDB: 1NLO).
Protein: DP03311 (UniProt P00740)
Region: residues 52	to 56
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 53 and 54 bind Ca+2 ions according to the crystal structure (PDB: 1NLO).
Protein: DP03311 (UniProt P00740)
Region: residues 52	to 56
Annotation: calcium ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 53 and 54 bind Ca+2 ions according to the crystal structure (PDB: 1NLO).
Cross-references: PDB:1NL0
Protein: DP03311 (UniProt P00740)
Region: residues 47	to 51
Annotation: calcium ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 47 and 48 bind Ca+2 ions according to the crystal structure (PDB: 1NLO).
Cross-references: PDB:1NL0
Protein: DP03311 (UniProt P00740)
Region: residues 47	to 51
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 47 and 48 bind Ca+2 ions according to the crystal structure (PDB: 1NLO).
Protein: DP03311 (UniProt P00740)
Region: residues 60	to 64
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 61 and 63 bind Ca+2 ions according to the crystal structure (PDB: 1NLO).
Protein: DP03311 (UniProt P00740)
Region: residues 60	to 64
Annotation: calcium ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 61 and 63 bind Ca+2 ions according to the crystal structure (PDB: 1NLO).
Cross-references: PDB:1NL0
Protein: DP03311 (UniProt P00740)
Region: residues 64	to 68
Annotation: calcium ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 66 and 67 bind Ca+2 ions according to the crystal structure (PDB: 1NLO).
Cross-references: PDB:1NL0
Protein: DP03311 (UniProt P00740)
Region: residues 64	to 68
Annotation: metal ion binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Residues 66 and 67 bind Ca+2 ions according to the crystal structure (PDB: 1NLO).
Protein: DP03312 (UniProt P10619)
Region: residues 288	to 327
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Coming from the N-terminus, the electron density around Pro258–Ser259 becomes progressively more disordered, and from around Met299–Asp300 towards the C-terminus, the electron density gets clear again. Blobs of density in between suggest that more residues of the activation loop are still present but not clearly visible due to disorder. 
Residues 260 to 299 (unmodelled in the PDB structure) correspond to residues 288-327 of the Uniprot sequence.
Cross-references: PDB:4CI9
Protein: DP03313 (UniProt P00488)
Region: residues 2	to 38
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
The [15N,1H]-HSQC spectra of the AP-FXIII in water revealed the presence of too many peaks, and the extra peaks were attributed to the presence of cis conformers about the Pro-peptide bonds. The presence of these additional peaks already indicated that AP-FXIII in water was mainly unstructured.
To assess whether segments of the polypeptide chain are folded, a 15N{1H}-NOE experiment was recorded. Typically, amide nitrogen atoms of well-structured regions adopt values larger than 0.5, whereas for fully flexible regions the values are negative. In our experience secondary structure can only be reliably determined by NMR if the H-NOE in the corresponding segment is larger than 0.4. Values of the 15N{1H}-NOE of AP-FXIII are depicted in Figure 5 for both environments. Clearly, no values larger than 0.4 are encountered, and for many residues the heteronuclear NOE is close to 0.2, indicating that they are not fully flexible but that structure determination using NMR is not possible.
These experiments indicated a high conformational flexibility of the peptide in both water and plasma environments, precluding a more detailed structural characterization by NMR.