LiteFold/DisProt huggingface dataset:
Protein: DP03347 (UniProt P10824)
Region: residues 2	to 32
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The amino-terminal 33 residues are disordered in GTP gamma S-Gi alpha 1, suggesting a mechanism that may promote release of the beta gamma subunit complex when the alpha subunit is activated by GTP. 
Although the Giα1 protein present in the crystals is intact, no electron density is observed for either the amino-terminal 32 residues or the carboxyl-terminal 11 residues.
Cross-references: PDB:1GIA
PDB:1GIL
PDB:1GFI
Protein: DP03347 (UniProt P10824)
Region: residues 343	to 354
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Although the Giα1 protein present in the crystals is intact, no electron density is observed for either the amino-terminal 32 residues or the carboxyl-terminal 11 residues.
Cross-references: PDB:1GIA
PDB:1GIL
PDB:1GFI
Protein: DP03347 (UniProt P10824)
Region: residues 11	to 32
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Structure of RGS4 bound to AlF4--activated Giα1: stabilization of the transition state for GTP hydrolysis.
Cross-references: PDB:1AGR
Protein: DP03347 (UniProt P10824)
Region: residues 343	to 354
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Structure of RGS4 bound to AlF4--activated Giα1: stabilization of the transition state for GTP hydrolysis.
Cross-references: PDB:1AGR
Protein: DP03348 (UniProt Q5T1C6)
Region: residues 81	to 106
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Them4 and Them5 proteins contain a highly variable sequence stretch (ca. residues 83 to 109 and ca. residues 91 to 114 for Them4 and Them5, respectively) that is partially disordered in both crystal structures.
According to PDB 4AE8 region that spans residues from 81 to 106 is disordered.
Cross-references: PDB:4AE8
Protein: DP03349 (UniProt P11795)
Region: residues 2	to 101
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-terminal, inward projecting R domain is flexibly tethered to the rest of the subunit: it therefore cannot be seen in the electron density map.
Region 2-101 is disordered in PDB chains B and C although in chain A only residues 2-67 are missing.
Cross-references: PDB:2TBV
Protein: DP03350 (UniProt P03316)
Region: residues 1	to 113
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 113 residues, as expected, are mostly disordered and account for much of the 'solvent' density. However, there is some electron density, corresponding to about 7  residues, whose assignment remains unknown.
Protein: DP03350 (UniProt P03316)
Region: residues 1	to 105
Annotation: disorder (Structural state)
Evidence: electron microscopy evidence used in manual assertion
Supporting statements:
Note that the amino-terminal residues 106 to 114 are out of density but that there is an obvious density region where these residues are positioned in the virus as opposed to the crystal structure.
Missing electron density from the PDB shows the region 1-105 as disordered.
Cross-references: PDB:1LD4
Protein: DP03350 (UniProt P03316)
Region: residues 1	to 105
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
These in turn surround a contiguous layer of density (yellow in Fig. 2b) that is mainly composed of the flexible CP N-terminal region (amino acids 1–113).
(b) Same as (a) but including the layer of unmodeled density that lies immediately below the ordered protease domain layer and is ascribed primarily to the disordered, 113-residue, N-terminal region of CP.
Missing electron density in the PDB shows that the 1-105 region is disordered.
Cross-references: PDB:3J0F
EMDB:EMD-525
Protein: DP03351 (UniProt P23677)
Region: residues 187	to 196
Annotation: order to disorder (Structural transition)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
The most striking conformational change induced by substrates/products is that the N-terminal portion comprising residues 187 to 196 becomes disordered, whereas it is a defined α-helix (α0N) in the apo form (Figure 3D).
Cross-references: PDB:1W2C
PDB:1W2D
PDB:1W2F
Protein: DP03351 (UniProt P23677)
Region: residues 187	to 196
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
The N-terminal residues form a small α0N helix in the apo-form (residues 187-196) that is disordered when substrates or products are bound.
IP3-3K has these structural elements except that the N lobe has helix α0N instead of an N-terminal β strand (Figure 1B) and that this region is disordered in the presence of bound ATP or ADP.
Cross-references: PDB:1W2D
PDB:1W2C
Protein: DP03351 (UniProt P23677)
Region: residues 187	to 196
Annotation: order (Structural state)
Evidence: X-ray crystallography-based structural model with high relative B-factor values used in manual assertion
Supporting statements:
The N-terminal residues form a small α0N helix in the apo-form (residues 187-196) that is disordered when substrates or products are bound.
The most striking conformational change induced by substrates/products is that the N-terminal portion comprising residues 187 to 196 becomes disordered, whereas it is a defined α-helix (α0N) in the apo form (Figure 3D).
Cross-references: PDB:1W2F
Protein: DP03353 (UniProt P05546)
Region: residues 20	to 79
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 the position  for  the  majority  of  the  acidic  tail  is  undefined  in the  structure  of  native  HCII.  Of  the 160  amino  acids  in  the N-terminal tails of the two molecules comprising the crystallographic asymmetric unit (Fig. 1 e ), only 11 can be unequivocally placed in density (Leu-61 – Asp-71).
Position 61 in the structure is residue 80 in the sequence and position 71 in the structure is residue 90 in the sequence.
Cross-references: PDB:1JMJ
Protein: DP03353 (UniProt P05546)
Region: residues 91	to 113
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
 the position  for  the  majority  of  the  acidic  tail  is  undefined  in the  structure  of  native  HCII.  Of  the 160  amino  acids  in  the N-terminal tails of the two molecules comprising the crystallographic asymmetric unit (Fig. 1 e ), only 11 can be unequivocally placed in density (Leu-61 – Asp-71).
Position 61 in the structure is residue 80 in the sequence and position 71 in the structure is residue 90 in the sequence.
Cross-references: PDB:1JMJ
Protein: DP03354 (UniProt P63144)
Region: residues 1	to 62
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
βN-(1–62) Does Not Exhibit a Defined Structure in Solution
Furthermore, experiments performed to determine the rates of H/D exchange of amide protons showed that all these protons were exchanged in <3 min., indicating that none of these protons are protected by formation of hydrogen bonds within an “internal structure.” Rather all amide protons are easily accessible from the solvent, as is typical for not compactly folded peptides. In summary, these results indicated that βN-(1–62) does not exhibit a well defined structure in solution, but rather behaves like a flexible peptide showing only transient formation of local structures.
βN-(1–62) is a nonstructured peptide.
As determined from NMR experiments, the hydrophilic N terminus of Kvβ1.1 does not exhibit a well defined, unique three-dimensional structure. Rather it can be described by a fast conformational equilibrium of weakly structured substates.
Protein: DP03354 (UniProt P63144)
Region: residues 1	to 62
Annotation: entropic chain (Disorder function)
Evidence: physical interaction evidence used in manual assertion
Supporting statements:
βN-(1–62) acts as an open channel blocker.
Kinetics of βN-(1-62)-mediated inactivation. A, inactivation of non-inactivating Kv1.1 channels mediated by 50 μm βN-(1–62) applied to the cytoplasmic side of a giant inside-out patch by the fast application system.
βN-(1–62) Interacts with the α-Subunit of Kv 1.1 Channels in a Ball-like Manner
The functional characteristics of βN-(1–62) were tested in inside-out patches from Xenopus oocytes expressing non-inactivating Kv1.1 channels. As shown in Fig. 1 B, βN-(1–62) induced rapid inactivation of these channels when present at 50 μm on the cytoplasmic side of the patch; the time-course of inactivation depended on the peptide concentration (not shown). βN-(1–62) blocked Kv1.1 channels only in the open state (Fig. 1 B), similar to IDs derived from Kvα subunits (6, 10).
The interaction between βN-(1–62) and the channel α-subunit was more closely investigated by the “fast application” technique. This technique (see “Materials and Methods”) allows solution exchange at giant inside-out patches in less than 2 ms and enables separate determination for on and off rates of channel-peptide interaction (8,24). Fig. 2, A andB, shows rapid application and wash-off of 50 μm βN-(1–62); these experiments were performed at a membrane potential of 0 mV under asymmetrical K+ conditions ([K+]ex 5 mm, [K+]in 120 mm). Inactivation occurred with a time constant of ≈10 ms (10.3 ± 1.6 ms,n = 3) and was the same whether determined by fast application (left panel, first activation) or in the continuous presence of βN-(1–62) (left, second activation).
The results presented here show that Kvβ1.1 mediates fast inactivation of Kv1α subunits via an N-type mechanism of inactivation. Accordingly, the unique N terminus of Kvβ1.1 comprises a ball-like domain that blocks the channel via interaction with a receptor site that becomes accessible upon channel opening.
Protein: DP03354 (UniProt P63144)
Region: residues 1	to 62
Annotation: protein binding (Molecular function)
Evidence: physical interaction evidence used in manual assertion
Supporting statements:
βN-(1–62) Interacts with the α-Subunit of Kv 1.1 Channels in a Ball-like Manner
The interaction between βN-(1–62) and the channel α-subunit was more closely investigated by the “fast application” technique. This technique (see “Materials and Methods”) allows solution exchange at giant inside-out patches in less than 2 ms and enables separate determination for on and off rates of channel-peptide interaction (8,24). Fig. 2, A andB, shows rapid application and wash-off of 50 μm βN-(1–62); these experiments were performed at a membrane potential of 0 mV under asymmetrical K+ conditions ([K+]ex 5 mm, [K+]in 120 mm). Inactivation occurred with a time constant of ≈10 ms (10.3 ± 1.6 ms,n = 3) and was the same whether determined by fast application (left panel, first activation) or in the continuous presence of βN-(1–62) (left, second activation).
The results presented here show that Kvβ1.1 mediates fast inactivation of Kv1α subunits via an N-type mechanism of inactivation. Accordingly, the unique N terminus of Kvβ1.1 comprises a ball-like domain that blocks the channel via interaction with a receptor site that becomes accessible upon channel opening.
Protein: DP03355 (UniProt P0ABJ3)
Region: residues 1	to 18
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Out of the 1,291 residues in cytochrome bo3 ubiquinol oxidase we could assign the sequence for 967 residues (subunit I, 52–81, 96–179, 186–488, 490–520 and 541–552; subunit II, 36–112 and 125–283; subunit III, 19–51, 66–124 and 134–203; subunit IV, 1–109).
Cross-references: PDB:1FFT
Protein: DP03357 (UniProt Q5SHN5)
Region: residues 40	to 67
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The so-called 'effector' region in the G domain is disordered and not visible in our maps (residues 38-68). This may reflect the functional flexibility of this region, which is possibly involved in interactions with the ribosome and under goes conformational changes upon GTP hydrolysis (Peter et al.,1990b).
Protein: DP03357 (UniProt Q5SHN5)
Region: residues 40	to 67
Annotation: molecular function regulator (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The so-called 'effector' region in the G domain is disordered and not visible in our maps (residues 38-68). This may reflect the functional flexibility of this region, which is possibly involved in interactions with the ribosome and under goes conformational changes upon GTP hydrolysis (Peter et al.,1990b).
The active GTPase interacts with the effector which may be identical to the GAP or different. GEF may not dissociate until GTP is bound (Boguski and McCormick, 1993), and more complicated interactions between GTPase and GEF may exist (Kaziro et al., 1991).
Protein: DP03358 (UniProt Q92743)
Region: residues 94	to 106
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-domain structure does not include residues Gly94-Gln106 due to disorder– the homologous IGFBP-4 residues form a short α-helix which contacts IGF-I.
N-domain molecules are tightly packed within the crystals – of the 118 amino acids in the final model (Gly36 to Ala154, not including Gly94-Gln106), 78 are within 4.5 Å of a neighboring molecule.
Cross-references: PDB:3TJQ
Protein: DP03358 (UniProt Q92743)
Region: residues 301	to 313
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Similarly to those of other HtrAs in the inactive state, the active-site loops L1, L2, L3 and LD are severely disordered, impeding the proper function of the catalytic triad, oxyanion hole and S1 specificity pocket (Fig. 1b,c)3,11–13.
Upon activation, loops L1, L2, L3 and LD undergo a disorder-to-order transition yielding a stably folded activation domain.
Some protein segments including residues 158-160, 285-289 (loop LD), 301-314 (loop L3), and 371-480 (PDZ domain) were hardly visible or invisible in these maps and were therefore omitted from the model.
Residues 301-313 (loop L3) are disordered in all ligand-free structures (PDB 3NWU and 3NUM).
Cross-references: PDB:3NUM
PDB:3NWU
Protein: DP03358 (UniProt Q92743)
Region: residues 301	to 313
Annotation: disorder to order (Structural transition)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Peptide binding is the allosteric activation signal that is transmitted to the protease domain via the sensor loop L3 (nomenclature according to refs. 2,3). Rearrangement of L3 induces the remodeling of the activation domain (loops L1, L2, LD) from the resting into the active conformation, which includes a functional catalytic triad, the oxyanion hole, and substrate-specificity pockets3,4.
Upon activation, loops L1, L2, L3 and LD undergo a disorder-to-order transition yielding a stably folded activation domain.
Our data indicate that ligand binding to the protease domain is sufficient to rearrange the activation domain and loop L3 because, in contrast to what occurs with other serine proteases, substrates interact directly with L3 and complete the activation domain. Therefore, the activity of HTRA1 is controlled by induced-fit substrate binding and does not depend on allosteric ligands acting in trans such as are seen with DegP or DegS4,11,17,19.
Residues 301-313 (loop L3) are disordered in all ligand-free structures (PDB 3NWU and 3NUM) and become ordered in the ligand-bound form of HTRA1 (PDB 3NZI).
Cross-references: PDB:3NUM
PDB:3NWU
PDB:3NZI
Protein: DP03358 (UniProt Q92743)
Region: residues 301	to 313
Annotation: molecular function activator activity (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
Peptide binding is the allosteric activation signal that is transmitted to the protease domain via the sensor loop L3 (nomenclature according to refs. 2,3). Rearrangement of L3 induces the remodeling of the activation domain (loops L1, L2, LD) from the resting into the active conformation, which includes a functional catalytic triad, the oxyanion hole, and substrate-specificity pockets3,4.
Similarly to those of other HtrAs in the inactive state, the active-site loops L1, L2, L3 and LD are severely disordered, impeding the proper function of the catalytic triad, oxyanion hole and S1 specificity pocket (Fig. 1b,c)3,11–13.
Upon activation, loops L1, L2, L3 and LD undergo a disorder-to-order transition yielding a stably folded activation domain.
Our data indicate that ligand binding to the protease domain is sufficient to rearrange the activation domain and loop L3 because, in contrast to what occurs with other serine proteases, substrates interact directly with L3 and complete the activation domain. Therefore, the activity of HTRA1 is controlled by induced-fit substrate binding and does not depend on allosteric ligands acting in trans such as are seen with DegP or DegS4,11,17,19.
Residues 301-313 (loop L3) are disordered in all ligand-free structures (PDB 3NWU and 3NUM) and become ordered in the ligand-bound form of HTRA1 (PDB 3NZI).
Cross-references: PDB:3NUM
PDB:3NWU
PDB:3NZI
Protein: DP03358 (UniProt Q92743)
Region: residues 301	to 313
Annotation: protein binding (Molecular function)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The bound ligand interacts closely with the sensor loop L3, contributing to the hydrophobic core of the activation domain involving residues Leu307, Leu309 and Tyr316 (loop L3), Leu345 and Thr344 along with P2-Leu and P4-Phe (Fig. 2b,c).
Residues in loop L3 forming hydrophobic interactions with the inhibitor molecule are shown in stick presentation (orange).
Our data indicate that ligand binding to the protease domain is sufficient to rearrange the activation domain and loop L3 because, in contrast to what occurs with other serine proteases, substrates interact directly with L3 and complete the activation domain. Therefore, the activity of HTRA1 is controlled by induced-fit substrate binding and does not depend on allosteric ligands acting in trans such as are seen with DegP or DegS4,11,17,19.
Curator statement: Residues 301-313 (loop L3) are disordered in all ligand-free structures (PDB 3NWU and 3NUM) and become ordered in the ligand-bound form of HTRA1 (PDB 3NZI).
Protein: DP03359 (UniProt P9WJD9)
Region: residues 290	to 460
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final structure revealed the N-terminal domain of EspB to be organized as a cylindrical heptamer with dimensions of 90 Å x 90 Å and a central channel of 45 Å diameter whereas the C-terminal domain was unstructured.

The linker (86 to 126) and the C-terminal (291 to 460) domains were not visible in the final map and consequently, the atomic reconstruction was not possible for those domains.
Cross-references: PDB:6XZC
Protein: DP03359 (UniProt P9WJD9)
Region: residues 86	to 126
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Indeed, for each monomer, the atomic model was accurately built from amino acids 8 to 85 corresponding to the PE domain, and from 127 to 290, corresponding to the PPE domain (Fig. 2B), thanks to a high quality density map at medium-resolution (Fig. S1). The linker (86 to 126) and the C-terminal (291 to 460) domains were not visible in the final map and consequently, the atomic reconstruction was not possible for those domains
Cross-references: PDB:6XZC
Protein: DP03359 (UniProt P9WJD9)
Region: residues 86	to 126
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Indeed, for each monomer, the atomic model was accurately built from amino acids 8 to 85 corresponding to the PE domain, and from 127 to 290, corresponding to the PPE domain (Fig. 2B), thanks to a high quality density map at medium-resolution (Fig. S1). The linker (86 to 126) and the C-terminal (291 to 460) domains were not visible in the final map and consequently, the atomic reconstruction was not possible for those domains
Cross-references: PDB:6XZC
Protein: DP03360 (UniProt Q56062)
Region: residues 119	to 129
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In both the native enzyme and pyruvate/Mg(2+) bound forms, the active site loop is completely disordered.
However, significant and unambiguous density was not found in three different places: the N terminal 3–4 residues; the active site loop between fourth β-strand and sixth α-helix (residues 118–129), and the last 6–13 C-terminal residues in different subunits.
In the present case, the active site loop, which includes the critical cysteine residue that acts as the base during catalysis, is completely disordered in both native as well as pyruvate/Mg2+ bound PrpB.
Cross-references: PDB:1O5Q
PDB:1UJQ
Protein: DP03360 (UniProt Q56062)
Region: residues 119	to 129
Annotation: molecular function activator activity (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In both the native enzyme and pyruvate/Mg(2+) bound forms, the active site loop is completely disordered.
However, significant and unambiguous density was not found in three different places: the N terminal 3–4 residues; the active site loop between fourth β-strand and sixth α-helix (residues 118–129), and the last 6–13 C-terminal residues in different subunits.
In the present case, the active site loop, which includes the critical cysteine residue that acts as the base during catalysis, is completely disordered in both native as well as pyruvate/Mg2+ bound PrpB.
Cross-references: PDB:1O5Q
PDB:1UJQ
Protein: DP03361 (UniProt Q8ZKB0)
Region: residues 2	to 34
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The additional N-terminal domain is disordered in our StYjeQ structure, but is designated as a probable ribosome-interaction domain (RID; residues 1–20; Fig. 1) on the basis of sequence homology with the equivalent region of EcYjeQ, in which it has been shown experimentally to play a critical role in the tight binding of EcYjeQ to the 30S ribosome (Daigle & Brown, 2004).
Cross-references: PDB:2RCN