LiteFold/DisProt huggingface dataset:
Protein: DP02653 (UniProt P61765)
Region: residues 295	to 358
Annotation: molecular adaptor activity (Molecular function)
Evidence: circular dichroism evidence used in manual assertion
Supporting statements:
Munc18-1 domain 3a may be flexible in the unbound solution state and adopt an ordered conformation upon interaction with binding partners. We showed that a domain 3a peptide interacts with preformed SNARE complex, as evidenced by an increase in helicity consistent with coiled-coil formation.
Domain 3a variability suggests this region may be unstructured in the unbound solution state and possibly adopts a helical structure upon interaction with partners
We identified a conformational change in Munc18-1 domain 3a (residues 295–358); these residues form the predominant interaction site with Sx1 helices H3 and Hc in the Munc18-1–Sx1 closed structure (6). In that structure, Munc18-1 residues 295–358 form a bent hairpin, but in the Munc18-1 structure reported here the hairpin is unfurled, involving a 180° rotation and > 25 Å translation of backbone residues to form an extended antiparallel helical hairpin.
The structure of N-peptide bound rat Munc18-1 adopts an extended domain 3a conformation that may preclude closed Sx1 binding yet remain compatible with binding open Sx1 and SNARE complexes.
Protein: DP02654 (UniProt Q9H5I1)
Region: residues 379	to 392
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Post-SET is fully structured only when bound to the substrate peptide (Figure 2A), or to a small molecule inhibitor [32], but the density is incomplete otherwise (Figure 2B–D). This implies that Post-SET is naturally flexible, which may be important for peptide turn-over, as recently proposed 
A flexible or even disordered state when no co-factor or peptide is bound.
Cross-references: PDB:2R3A
Protein: DP02655 (UniProt Q8ZQC8)
Region: residues 1	to 35
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Note that the electron density for the first 75 residues in both proteins is not contiguous and only several helical segments could be modeled
The residues of the N-terminal segmentare not well defined displaying high flexibility
Cross-references: PDB:5CQ9
Protein: DP02655 (UniProt Q8ZQC8)
Region: residues 64	to 74
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Note that the electron density for the first 75 residues in both proteins is not contiguous and only several helical segments could be modeled
The residues of the N-terminal segmentare not well defined displaying high flexibility
Cross-references: PDB:5CQ9
Protein: DP02656 (UniProt P08294)
Region: residues 19	to 54
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N- and C-terminal end regions required for tetramerisation and heparin binding, respectively, are highly flexible.
Both the N- and the C-terminal ends are incomplete in the structural model reported here, as there is weak electron density corresponding to these regions (modelling at 0.7σ contour level was not reliable), signifying either a greater flexibility for these parts of the molecule or the possibility that the protein has partially degraded during crystallisation.
The functionally important C- and N-terminal end regions are found to be highly flexible and are not fully visible in the electron density.
Cross-references: PDB:2JLP
Protein: DP02656 (UniProt P08294)
Region: residues 19	to 54
Annotation: molecular adaptor activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N- and C-terminal end regions required for tetramerisation and heparin binding, respectively, are highly flexible.
Both the N- and the C-terminal ends are incomplete in the structural model reported here, as there is weak electron density corresponding to these regions (modelling at 0.7σ contour level was not reliable), signifying either a greater flexibility for these parts of the molecule or the possibility that the protein has partially degraded during crystallisation.
The functionally important C- and N-terminal end regions are found to be highly flexible and are not fully visible in the electron density.
Among the missing residues at the N-terminus is Val24, which is known to be involved in oligomerisation of SOD3; in particular, the mutation Val to Asp in tetrameric mouse SOD3 causes it to become dimeric, while the reverse mutation in natively dimeric rat SOD3 converts it to a tetramer
Cross-references: PDB:2JLP
Protein: DP02656 (UniProt P08294)
Region: residues 224	to 240
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N- and C-terminal end regions required for tetramerisation and heparin binding, respectively, are highly flexible.
Both the N- and the C-terminal ends are incomplete in the structural model reported here, as there is weak electron density corresponding to these regions (modelling at 0.7σ contour level was not reliable), signifying either a greater flexibility for these parts of the molecule or the possibility that the protein has partially degraded during crystallisation.
The functionally important C- and N-terminal end regions are found to be highly flexible and are not fully visible in the electron density.
Cross-references: PDB:2JLP
Protein: DP02656 (UniProt P08294)
Region: residues 224	to 240
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N- and C-terminal end regions required for tetramerisation and heparin binding, respectively, are highly flexible.
Both the N- and the C-terminal ends are incomplete in the structural model reported here, as there is weak electron density corresponding to these regions (modelling at 0.7σ contour level was not reliable), signifying either a greater flexibility for these parts of the molecule or the possibility that the protein has partially degraded during crystallisation.
The functionally important C- and N-terminal end regions are found to be highly flexible and are not fully visible in the electron density.
Cross-references: PDB:2JLP
Protein: DP02657 (UniProt O88483)
Region: residues 375	to 385
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Some of the solvent-exposed parts of the PDP1c molecule are disordered and not included in the model. These are the residues 111–114, 152–157, 304–314, 374–404 and 418–442 that probably form flexible loops in the PDP1c molecule.
Region 304-314 missing from the model corresponds to region 375-385 of the sequence
Cross-references: PDB:2PNQ
Protein: DP02657 (UniProt O88483)
Region: residues 445	to 475
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Some of the solvent-exposed parts of the PDP1c molecule are disordered and not included in the model. These are the residues 111–114, 152–157, 304–314, 374–404 and 418–442 that probably form flexible loops in the PDP1c molecule.
Region 374-404 missing from the model corresponds to region 445-475 of the sequence
Cross-references: PDB:2PNQ
Protein: DP02658 (UniProt Q8N807)
Region: residues 21	to 31
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although we used recombinant hPDILT protein consisting of amino acids Ser-21–Val-580 for crystal growth (Fig. 2A), only amino acids Ser-32–Lys-495 are clearly distinguished in the final electron density map, covering parts of the N-terminal loop, four thioredoxin-like domains (a, b, b′, and a′), and the x-linker (Fig. 2B).
Cross-references: PDB:5XF7
Protein: DP02658 (UniProt Q8N807)
Region: residues 21	to 44
Annotation: protein folding chaperone (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although we used recombinant hPDILT protein consisting of amino acids Ser-21–Val-580 for crystal growth (Fig. 2A), only amino acids Ser-32–Lys-495 are clearly distinguished in the final electron density map, covering parts of the N-terminal loop, four thioredoxin-like domains (a, b, b′, and a′), and the x-linker (Fig. 2B).
The full-length hPDILT consisting of 584 amino acids divided into 9 regions, including the signal peptide (Met-1–Ser-20), N-terminal loop (Ser-21–Ser-44), a domain (Leu-45–Lys-155), b domain (Ala-156–Thr-255), b′ domain (Asp-256–Lys-369), x-linker (Asn-370–Leu-388), a′ domain (Val-389–Lys-496), C-terminal tail (Ile-497–Val-580), and the ER retrieval peptide KEEL (Lys-581–Leu-584) (Fig. 1A).
Thus, the N-terminal loop and the C-terminal tails are important for the chaperone activity. 
Cross-references: PDB:5XF7
Protein: DP02658 (UniProt Q8N807)
Region: residues 496	to 580
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although we used recombinant hPDILT protein consisting of amino acids Ser-21–Val-580 for crystal growth (Fig. 2A), only amino acids Ser-32–Lys-495 are clearly distinguished in the final electron density map, covering parts of the N-terminal loop, four thioredoxin-like domains (a, b, b′, and a′), and the x-linker (Fig. 2B).
The full-length hPDILT consisting of 584 amino acids divided into 9 regions, including the signal peptide (Met-1–Ser-20), N-terminal loop (Ser-21–Ser-44), a domain (Leu-45–Lys-155), b domain (Ala-156–Thr-255), b′ domain (Asp-256–Lys-369), x-linker (Asn-370–Leu-388), a′ domain (Val-389–Lys-496), C-terminal tail (Ile-497–Val-580), and the ER retrieval peptide KEEL (Lys-581–Leu-584) (Fig. 1A).
This result suggests that the C-terminal tail of hPDILT is flexible in the crystal structure.
Cross-references: PDB:5XF7
Protein: DP02658 (UniProt Q8N807)
Region: residues 496	to 580
Annotation: protein folding chaperone (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although we used recombinant hPDILT protein consisting of amino acids Ser-21–Val-580 for crystal growth (Fig. 2A), only amino acids Ser-32–Lys-495 are clearly distinguished in the final electron density map, covering parts of the N-terminal loop, four thioredoxin-like domains (a, b, b′, and a′), and the x-linker (Fig. 2B).
The full-length hPDILT consisting of 584 amino acids divided into 9 regions, including the signal peptide (Met-1–Ser-20), N-terminal loop (Ser-21–Ser-44), a domain (Leu-45–Lys-155), b domain (Ala-156–Thr-255), b′ domain (Asp-256–Lys-369), x-linker (Asn-370–Leu-388), a′ domain (Val-389–Lys-496), C-terminal tail (Ile-497–Val-580), and the ER retrieval peptide KEEL (Lys-581–Leu-584) (Fig. 1A).
This result suggests that the C-terminal tail of hPDILT is flexible in the crystal structure.
Thus, the N-terminal loop and the C-terminal tails are important for the chaperone activity.
Cross-references: PDB:5XF7
Protein: DP02659 (UniProt Q91ZW2)
Region: residues 255	to 267
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Twenty-nine POFUT1 residues belonging to three segments (79–87, 255–267, and 275–281) flanking the binding groove are disordered in the POFUT1–GDP binary complex, but ordered, to different degrees, upon EGF-LD binding.
Cross-references: PDB:5KY0
PDB:5KXH
PDB:5KY3
PDB:5KY4
PDB:5KY7
Protein: DP02660 (UniProt Q9SKB2)
Region: residues 225	to 270
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal cap features a highly positively charged linear motif which was found to be largely disordered in this structure.
In line with this, the C-terminal capping domain, which in plant LRR-RKs is normally terminated by a well defined disulfide bond (Hohmann et al., 2017), is found to be largely disordered in our SOBIR1 structure
Cross-references: PDB:6R1H
Protein: DP02661 (UniProt Q6ZVN8)
Region: residues 130	to 145
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This resulted in a well-defined model for the RGMCND–BMP2 complex that included two molecules of RGMC (residues Q36–P129) bound to a disulfide linked BMP2 dimer (residues K293–R396)
Each RGMBND is connected to the RGMB C-terminal domain (RGMBCD) via a disordered 15 amino acid linker not visible in the electron density map.
Cross-references: PDB:4UI1
Protein: DP02661 (UniProt Q6ZVN8)
Region: residues 130	to 145
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Each RGMBND is connected to the RGMB C-terminal domain (RGMBCD) via a disordered 15 amino acid linker not visible in the electron density map.
Cross-references: PDB:4UI1
Protein: DP02662 (UniProt Q9VXJ0)
Region: residues 44	to 55
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In total, 80% of the total sequence was comprised of the clear density that initially enabled the tracking of the correct position of the atoms in the main chain; however, the density was poor in some areas of the map that are known to contain flexible regions in the homologous structures. The missing polypeptide fragments included regions 1–6, 44–55, 88–98 and 200–204 in the dehydrogenase domain, and 373–387, 451–457 and 593–598 in the hydratase domain.
missing region inside the dehydrogenase domain (1–307)
Cross-references: PDB:3OML
Protein: DP02662 (UniProt Q9VXJ0)
Region: residues 88	to 98
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In total, 80% of the total sequence was comprised of the clear density that initially enabled the tracking of the correct position of the atoms in the main chain; however, the density was poor in some areas of the map that are known to contain flexible regions in the homologous structures. The missing polypeptide fragments included regions 1–6, 44–55, 88–98 and 200–204 in the dehydrogenase domain, and 373–387, 451–457 and 593–598 in the hydratase domain.
missing region inside the dehydrogenase domain (1–307)
Cross-references: PDB:3OML
Protein: DP02662 (UniProt Q9VXJ0)
Region: residues 373	to 387
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In total, 80% of the total sequence was comprised of the clear density that initially enabled the tracking of the correct position of the atoms in the main chain; however, the density was poor in some areas of the map that are known to contain flexible regions in the homologous structures. The missing polypeptide fragments included regions 1–6, 44–55, 88–98 and 200–204 in the dehydrogenase domain, and 373–387, 451–457 and 593–598 in the hydratase domain.
missing region inside the hydratase domain (314–598)
Cross-references: PDB:3OML
Protein: DP02663 (UniProt P0A9Q9)
Region: residues 232	to 242
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure is too disordered to model from residues 232 to 242 in subunit A, from  residues 232 to 241 in subunit B, and from residues 233 to 240 in subunit C
Cross-references: PDB:1BRM
Protein: DP02664 (UniProt Q81G39)
Region: residues 397	to 413
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The crystal structure of DltA in the absence of any substrate was observed to have a noticeably more disordered pocket for ATP which would explain why DltA has relatively low affinity for ATP in the absence of any D-alanyl carrier.
We also determined the structure of BcDltA in the absence of any substrate. This structure is noticeably more disordered than previously reported DltA structures, which may explain the enzyme’s lower affinity to ATP in the absence of the other two substrates.
The electron density map indicated several disordered regions (Ser-153 to Pro-159, Pro-363 to Glu-367, Arg-397 to Glu-413, Lys-433 to Tyr-440) with the corresponding regions in the starting model highlighted in magenta in Figure 2B.
Cross-references: PDB:4PZP
Protein: DP02664 (UniProt Q81G39)
Region: residues 397	to 413
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density map indicated several disordered regions (Ser-153 to Pro-159, Pro-363 to Glu-367, Arg-397 to Glu-413, Lys-433 to Tyr-440) with the corresponding regions in the starting model highlighted in magenta in Figure 2B.
The C-terminal part of this flexible inter-domain region also contains a β-hairpin which has been observed to interact with CoA in homologous acetyl-CoA synthetase
The longest such disordered region is between Arg-397 and Glu-413, which contains the inter-domain hinge residue Asp-399, interacts with β-phosphate of ATP, and forms the pantetheine channel. Possibly, this important region remains disordered in the presence of saturating D-alanine, therefore providing an explanation for the similar values between the above mentioned K D (0.43 mM) and the K M (0.46 mM) for ATP, in the presence of saturating D-alanine but in absence of CoA.
Cross-references: PDB:4PZP
Protein: DP02665 (UniProt Q9Y5C1)
Region: residues 420	to 429
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
There are 3 monomers of Angptl3 in the asymmetric unit. The N-terminal His-tag as well as the C-terminal 6 amino acids are not visible. In addition, there are two regions within the fibrinogen-like domain (Lys389 - His391 and Pro420 - Arg429 in the A-chain) for which the electron density is either missing or not of sufficient quality to allow tracing of the chain, suggesting the presence of flexible loops.
Cross-references: PDB:6EUA
Protein: DP02667 (UniProt P41780)
Region: residues 20	to 31
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues not included due to the absence of any electron density include chain A (20-31, 349-356), chain B (20-32, 234-240, 349-356), chain C (20-25, 349-356), and chain D (20-32, 235-240, 350-356).
Cross-references: PDB:3PND
Protein: DP02668 (UniProt Q44522)
Region: residues 167	to 179
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered region—including loop segment 166–182 (AK6b), 167–179 (AB6b), or 70–76 (AtARF)—was not included in the model.
The acidic loop (residues 164–184), which may serve as a structural scaffold for protein–protein or protein–nucleic acid interaction, is disordered in both the AK6b and AB6b structures.
Cross-references: PDB:3AQ2
Protein: DP02669 (UniProt Q57530)
Region: residues 166	to 182
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The disordered region—including loop segment 166–182 (AK6b), 167–179 (AB6b), or 70–76 (AtARF)—was not included in the model.
The acidic loop (residues 164–184), which may serve as a structural scaffold for protein–protein or protein–nucleic acid interaction, is disordered in both the AK6b and AB6b structures.
Cross-references: PDB:3AQ3
Protein: DP02669 (UniProt Q57530)
Region: residues 164	to 184
Annotation: molecular function regulator (Molecular function)
Evidence: immunodetection assay evidence used in manual assertion
Supporting statements:
Acidic Region of the 6b Protein Is Required for Callus Formation and Shoot Regeneration on Hormone-Free Medium
The Acidic Region of the 6b Protein Is Essential for the Hormone-Independent Formation of Callus and the Interaction with NtSIP1
Analysis of the Role of the Acidic Region of 6b in the Interaction of 6b with NtSIP1 Using the Yeast Two-Hybrid System.
These results showed that the GALDBD-6b protein was capable of activating transcription and that the acidic region of 6b was required for activation
6b Protein Affects the Transcription of Plant Genes
The  6b  protein  did  not  include  any  obvious  DNA  binding motif, but it did include an acidic region that is required for its  interaction  with  NtSIP1  and  for  the  activation  of  transcription by 6b. Thus, 6b might function as a transcriptional coactivator/mediator  by  interacting  with  other  proteins  in the  transcriptional  machinery.
Protein: DP02669 (UniProt Q57530)
Region: residues 164	to 184
Annotation: protein binding (Molecular function)
Evidence: yeast 2-hybrid evidence used in manual assertion
Supporting statements:
The Acidic Region of the 6b Protein Is Essential for the Hormone-Independent Formation of Callus and the Interaction with NtSIP1
Analysis of the Role of the Acidic Region of 6b in the Interaction of 6b with NtSIP1 Using the Yeast Two-Hybrid System.
The  6b  protein  did  not  include  any  obvious  DNA  binding motif, but it did include an acidic region that is required for its  interaction  with  NtSIP1  and  for  the  activation  of  transcription by 6b. Thus, 6b might function as a transcriptional coactivator/mediator  by  interacting  with  other  proteins  in the  transcriptional  machinery.
Protein: DP02669 (UniProt Q57530)
Region: residues 164	to 184
Annotation: protein binding (Molecular function)
Evidence: immunodetection assay evidence used in manual assertion
Supporting statements:
The Acidic Region of the 6b Protein Is Essential for the Hormone-Independent Formation of Callus and the Interaction with NtSIP1
NtSIP1 Interacts with 6b in Vitro
The  6b  protein  did  not  include  any  obvious  DNA  binding motif, but it did include an acidic region that is required for its  interaction  with  NtSIP1  and  for  the  activation  of  transcription by 6b. Thus, 6b might function as a transcriptional coactivator/mediator  by  interacting  with  other  proteins  in the  transcriptional  machinery.