LiteFold/DisProt huggingface dataset:
Protein: DP02741 (UniProt P09951)
Region: residues 53	to 58
Annotation: glycosylation display site (Disorder function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Here, we identified seven in vivo O-GlcNAcylation sites on synapsin I by analysis of HPLC-purified digests of rat brain synapsin I. The seven O-GlcNAcylation sites (Ser55, Thr56, Thr87, Ser516, Thr524, Thr562, and Ser576) in synapsin I are clustered around its five phosphorylation sites in domains B and D.
The glycosylated sites correspond to Ser55 and Thr56.
Protein: DP02741 (UniProt P09951)
Region: residues 85	to 89
Annotation: glycosylation display site (Disorder function)
Evidence: chromatography evidence used in manual assertion
Supporting statements:
Here, we identified seven in vivo O-GlcNAcylation sites on synapsin I by analysis of HPLC-purified digests of rat brain synapsin I. The seven O-GlcNAcylation sites (Ser55, Thr56, Thr87, Ser516, Thr524, Thr562, and Ser576) in synapsin I are clustered around its five phosphorylation sites in domains B and D.
The glycosylated site correspond to Thr87.
Protein: DP02742 (UniProt P06756)
Region: residues 868	to 897
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was observed for TM residues and much of the α(V) linker. α(V)β(3)-AB and α(V)β(3)-1TM demonstrate flexibility in the linker between their extracellular and TM domains, rather than the previously proposed rigid linkage.
Cross-references: PDB:4G1M
Protein: DP02742 (UniProt P06756)
Region: residues 868	to 897
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
No electron density was observed for TM residues and much of the α(V) linker. α(V)β(3)-AB and α(V)β(3)-1TM demonstrate flexibility in the linker between their extracellular and TM domains, rather than the previously proposed rigid linkage.
Cross-references: PDB:4G1M
Protein: DP02743 (UniProt P97675)
Region: residues 324	to 336
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Its structure at 2.77 Å resolution reveals that the active-site zinc ions are missing and a large part of the active site and the surrounding residues are flexible.
However, owing to significant disorder and the low resolution of the data, model building and refinement of the NPP 349–875 structure reported here was only possible using the superimposed PDE and nuclease domains of the refined NPP3 140–875 structure as a starting point.
In all four chains of the NPP 349–875 structure the following regions of the PDE domain have no density owing to flexibility: 168–181, 324–336 and 473–492 (Fig. 2b).
Cross-references: PDB:6G4G
Protein: DP02743 (UniProt P97675)
Region: residues 473	to 492
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Its structure at 2.77 Å resolution reveals that the active-site zinc ions are missing and a large part of the active site and the surrounding residues are flexible.
However, owing to significant disorder and the low resolution of the data, model building and refinement of the NPP 349–875 structure reported here was only possible using the superimposed PDE and nuclease domains of the refined NPP3 140–875 structure as a starting point.
In all four chains of the NPP 349–875 structure the following regions of the PDE domain have no density owing to flexibility: 168–181, 324–336 and 473–492 (Fig. 2b).
Cross-references: PDB:6G4G
Protein: DP02744 (UniProt Q92574)
Region: residues 978	to 992
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 39 residues of each TSC1 helix (residues 939–977) formed a single helix, whereas the last 15 residues were not visible in our electron density map.
Cross-references: PDB:5EJC
Protein: DP02744 (UniProt Q92574)
Region: residues 939	to 992
Annotation: protein binding (Molecular function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
To reveal how TBC1D7 interacts with TSC1, we determined the crystal structure of the TSC1 TBC1D7-binding domain (residues 939–992) in complex with near full-length TBC1D7(19–293), using the Se-Met single wavelength anomalous dispersion method
Cross-references: PDB:5EJC
Protein: DP02744 (UniProt Q92574)
Region: residues 939	to 992
Annotation: protein binding (Molecular function)
Evidence: isothermal titration calorimetry evidence used in manual assertion
Supporting statements:
ITC showed that full-length TBC1D7 and N-terminal truncated TBC1D7 (residues 19–293) interacted with TSC1(939–992) with comparable affinities: 0.4 and 0.2 μm, respectively
Protein: DP02744 (UniProt Q92574)
Region: residues 939	to 992
Annotation: protein binding (Molecular function)
Evidence: bait-prey hybrid interaction evidence used in manual assertion
Supporting statements:
Pulldown experiments using the purified proteins showed that TSC1(939–992) was sufficient for interacting with TBC1D7 (Fig. 1a). TBC1D7 and TSC1(939–992) formed a stable complex and co-migrated in SEC.
Protein: DP02744 (UniProt Q92574)
Region: residues 939	to 992
Annotation: TSC1-TSC2 complex (Cellular component)
Evidence: x-ray crystallography evidence used in manual assertion
Supporting statements:
The TSC1-TBC1D7 interaction is important for the stability and activity of the TSC complex, a crucial regulator of the mTORC1 pathway that controls cell growth (25). Here we reveal the structural basis of the TSC1-TBC1D7 interaction.
Cross-references: PDB:5EJC
Protein: DP02745 (UniProt P05231)
Region: residues 28	to 46
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Although the amino-terminal 19 amino acids are disordered in solution, the remainder of the molecule has a well defined structure that shares many features displayed by other long-chain four-helix bundle cytokines.
Essentially all restraints are localized to residues 20 to 185; we have reported that the amino-terminal 19 residues of IL-6 are extremely flexible, as evidenced by observed 15N T2 values (Xu et al., 1996), and thus fail to yield any restraints useful for 3D structure determination.
The disordered N-terminal 19 residues correspond to the region 28-46 of the protein, since the authors cloned the gene lacking its signal peptide.
Cross-references: PDB:1IL6
PDB:2IL6
Protein: DP02745 (UniProt P05231)
Region: residues 28	to 46
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The N-termini of IL-6 and G-CSF are disordered so that the crystal structures of both begin at the start of helix A, whereas the N-terminal residues of hGH are ordered and are involved in receptor binding.
Cross-references: PDB:1ALU
Protein: DP02746 (UniProt Q14565)
Region: residues 271	to 289
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the L2 regions (shown in blue in Fig. 1 [triangle]), the full-length HsDMC1 structure has a slightly larger section of disordered amino-acid residues (residues 271–289).
Cross-references: PDB:4HYY
Protein: DP02746 (UniProt Q14565)
Region: residues 271	to 289
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
About 30% of the Dmc1 protein (the N-terminal region, Dmc11–82, and the putative DNA binding region (Loop 2), Dmc1 271–289) was uninterpretable from the calculated electron density maps, suggesting that these regions are either highly flexible or have multiple conformations.
Cross-references: PDB:1V5W
Protein: DP02746 (UniProt Q14565)
Region: residues 1	to 82
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
About 30% of the Dmc1 protein (the N-terminal region, Dmc1 1–82, and the putative DNA binding region (Loop 2), Dmc1 271–289) was uninterpretable from the calculated electron density maps, suggesting that these regions are either highly flexible or have multiple conformations.
Cross-references: PDB:1V5W
Protein: DP02747 (UniProt Q9GZN7)
Region: residues 47	to 56
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Residues 11 to 23, 47 to 56, 64 to 68, 92 to 96, 130 to 138, and 266 were not modelled due to weak electron density.
Cross-references: PDB:5XQH
Protein: DP02748 (UniProt P36871)
Region: residues 256	to 267
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In an apparent series of propagated changes, several other nearby loops are also disordered, including another in D1 (residues 64–65) and a larger region in D2 (residues 256–267). In total, 23 residues in two domains are affected by induced disorder in the structure of G291R mutant
Through comparison with the high-resolution crystal structure of wild-type (WT) human PGM1, also reported here, we find that both mutant enzymes suffer from regions of induced structural disorder and other effects resulting from the dramatic change in physicochemical characteristics at the site of mutation.
Two independent glycine to arginine substitutions (G121R and G291R), both affecting key active site loops of PGM1, are found to induce regions of structural disorder, as evidenced by a nearly complete loss of electron density for as many as 23 amino acids.
Cross-references: PDB:5HSH
Protein: DP02749 (UniProt P09041)
Region: residues 372	to 386
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Binding 3PG causes a 13 degree rotation that partially closes the structure and causes helix 13, which is disordered in the unliganded structure, to stabilize.
Residues 372–386 are disordered in the monomer bound with 3PG, similar to the unliganded PGK2 structure; however, these residues are clearly ordered, forming a helix, in the monomer with ATP bound.
Cross-references: PDB:2P9Q
Protein: DP02749 (UniProt P09041)
Region: residues 372	to 386
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Binding 3PG causes a 13 degree rotation that partially closes the structure and causes helix 13, which is disordered in the unliganded structure, to stabilize.
Binding ATP leaves the protein in the open configuration but also causes helix 13 to be ordered.
Residues 372–386 are disordered in the monomer bound with 3PG, similar to the unliganded PGK2 structure; however, these residues are clearly ordered, forming a helix, in the monomer with ATP bound.
Cross-references: PDB:2PAA
Protein: DP02750 (UniProt P17109)
Region: residues 472	to 488
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The residues Gly472 to Phe488 of the active site region are either disordered, or in an open conformation in the MenD oxoglutarate complex structure, but adopt a closed conformation in the MenD ThDP complex structure.
The most significant difference between the oxoglutarate complex and the ThDP complex structure, presumably caused by the binding of ThDP, is the movement of the loop (Tyr489 to Asn494) and the disorder region Gly472 to Phe488
Active site pocket of EcMenD anchoring ThDP and Mg2+ shows a disordered region in the apo and oxoglutarate complex structures, and an ordered region in the ThDP complex structure.
Cross-references: PDB:3HWW
Protein: DP02750 (UniProt P17109)
Region: residues 472	to 488
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The residues Gly472 to Phe488 of the active site region are either disordered, or in an open conformation in the MenD oxoglutarate complex structure, but adopt a closed conformation in the MenD ThDP complex structure.
Active site pocket of EcMenD anchoring ThDP and Mg2+ shows a disordered region in the apo and oxoglutarate complex structures, and an ordered region in the ThDP complex structure.
The most significant difference between the oxoglutarate complex and the ThDP complex structure, presumably caused by the binding of ThDP, is the movement of the loop (Tyr489 to Asn494) and the disorder region Gly472 to Phe488
Cross-references: PDB:3HWX
Protein: DP02750 (UniProt P17109)
Region: residues 472	to 488
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The region between β15 and α21, residue 472–488 (A chain) and residue 471–493 (B chain) is found disorder or have a weak density map, corresponding to the high flexible loop binding region for the cofactor ThDP.
Cross-references: PDB:3FLM
Protein: DP02751 (UniProt Q03653)
Region: residues 217	to 232
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The final model, which includes residues 9–562 of Efr3-N8–562 except for a disordered loop comprising residues 217–232, was refined to Rwork = 23.11% and Rfree = 25.56% with good geometry
Cross-references: PDB:4N5A
Protein: DP02752 (UniProt P46951)
Region: residues 470	to 483
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Ypp1 structure comprises residues 12–817, except for disordered loops spanning residues 131–134, 470–483, 714–741, and 788–790. Residues in several additional loops (residues 608–617, 661–666, and 680–683) could not be modeled in some of the other Ypp1 molecules within the unit cell. The structure was refined to Rwork = 23.98% and Rfree = 27.72% with good geometry
Cross-references: PDB:4N5C
Protein: DP02752 (UniProt P46951)
Region: residues 714	to 741
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Ypp1 structure comprises residues 12–817, except for disordered loops spanning residues 131–134, 470–483, 714–741, and 788–790. Residues in several additional loops (residues 608–617, 661–666, and 680–683) could not be modeled in some of the other Ypp1 molecules within the unit cell. The structure was refined to Rwork = 23.98% and Rfree = 27.72% with good geometry
Cross-references: PDB:4N5C
Protein: DP02753 (UniProt Q13617)
Region: residues 117	to 134
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Structural comparison of Cul2 with other cullin proteins reveals that they share a conserved cullin repeat structure and contain flexible N termini which play different roles in CRL formation
To investigate how VHL recruits Cul2, we co-expressed VHL (residues 1–213), EloB (residues 1–118), EloC (residues 17–112) and an N-terminal segment of Cul2 (Cul2N) spanning the first cullin repeat (residues 1–163), the minimal domain required for binding to VHL
Cross-references: PDB:4WQO
Protein: DP02753 (UniProt Q13617)
Region: residues 117	to 134
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
These residues could not be modeled, but was not mention in the text.
Cross-references: PDB:5N4W
Protein: DP02753 (UniProt Q13617)
Region: residues 625	to 634
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In our structure, some residues at the CTD (625–634 and 645–660) were disordered and could not be modeled.
Cross-references: PDB:5N4W
Protein: DP02753 (UniProt Q13617)
Region: residues 645	to 660
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In our structure, some residues at the CTD (625–634 and 645–660) were disordered and could not be modeled.
Cross-references: PDB:5N4W
Protein: DP02754 (UniProt Q9S7B5)
Region: residues 347	to 363
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In addition, a loop between residues 347 and 363 is disordered.
Apart from the disordered area (loop 347–363), this region in TS has the same fold as in the other enzymes.
Cross-references: PDB:1E5X
Protein: DP02755 (UniProt Q69ZK9)
Region: residues 159	to 172
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 NL2A reveals that the A splice insertion, which encompasses residues 152–169, is positioned in the β6–β7 loop. The inserted sequence is mostly disordered in the structure; electron density is observed only for residues 152–158 in one protomer and is entirely absent in the other
In the NL2A structure, the majority of the 17 residues inserted at the A site are disordered, making it difficult to predict the potential contribution of the A insert to NRX binding at this time.
Cross-references: PDB:3BL8
Protein: DP02756 (UniProt P21447)
Region: residues 627	to 686
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The function of P-gp requires the flexibility of its two halves, which are joined by a mobile linker that is disordered in all mP-gp structures reported so far.
Cross-references: PDB:5KPI
Protein: DP02756 (UniProt P21447)
Region: residues 627	to 686
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The function of P-gp requires the flexibility of its two halves, which are joined by a mobile linker that is disordered in all mP-gp structures reported so far.
Cross-references: PDB:5KPI
Protein: DP02756 (UniProt P21447)
Region: residues 627	to 683
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker (residues 627–683) between NBD1 and TM7 is not observed and presumed to be disordered. Residues 1–33 and 1272–1276 at the N- and C- termini are also not observed.
The N-terminal half of the protein (blue) and the C-terminal half (yellow) are connected by a flexible linker region (black dashed line) that is disordered in the structure.
Cross-references: PDB:4KSC
PDB:4KSB
PDB:4KSD
Protein: DP02756 (UniProt P21447)
Region: residues 627	to 683
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The linker (residues 627–683) between NBD1 and TM7 is not observed and presumed to be disordered. Residues 1–33 and 1272–1276 at the N- and C- termini are also not observed.
The N-terminal half of the protein (blue) and the C-terminal half (yellow) are connected by a flexible linker region (black dashed line) that is disordered in the structure.
Cross-references: PDB:4KSC
PDB:4KSB
PDB:4KSD
Protein: DP02757 (UniProt Q9GZU1)
Region: residues 1	to 59
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density is clearly resolved for residues 60–526 in the apo TRPML1 and residues 38–526 in the ML-SA1-bound TRPML1 (Extended Data Fig. 4), with the exception of a short linker in the luminal domain (amino acids 206–215).
Cross-references: PDB:5WJ5
Protein: DP02757 (UniProt Q9GZU1)
Region: residues 206	to 215
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density is clearly resolved for residues 60–526 in the apo TRPML1 and residues 38–526 in the ML-SA1-bound TRPML1 (Extended Data Fig. 4), with the exception of a short linker in the luminal domain (amino acids 206–215).
Cross-references: PDB:5WJ5
PDB:5WJ9
Protein: DP02757 (UniProt Q9GZU1)
Region: residues 527	to 580
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron density is clearly resolved for residues 60–526 in the apo TRPML1 and residues 38–526 in the ML-SA1-bound TRPML1 (Extended Data Fig. 4), with the exception of a short linker in the luminal domain (amino acids 206–215).
Cross-references: PDB:5WJ5
PDB:5WJ9
Protein: DP02757 (UniProt Q9GZU1)
Region: residues 206	to 215
Annotation: flexible linker (Disorder function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The electron density is clearly resolved for residues 60–526 in the apo TRPML1 and residues 38–526 in the ML-SA1-bound TRPML1 (Extended Data Fig. 4), with the exception of a short linker in the luminal domain (amino acids 206–215).
Cross-references: PDB:5WJ5
PDB:5WJ9
Protein: DP02757 (UniProt Q9GZU1)
Region: residues 573	to 578
Annotation: localization (Biological process)
Evidence: immunodetection assay evidence used in manual assertion
Supporting statements:
We have also found that the C-terminal tail of mucolipin-1 is palmitoylated and that this modification might regulate the efficiency of endocytosis. Finally, the mutagenesis of both di-leucine motifs abrogated lysosomal accumulation and resulted in cell-surface redistribution of mucolipin-1. Taken together, these results reveal novel information regarding the motifs that regulate mucolipin-1 trafficking and suggest a role for palmitoylation in protein sorting.
These data indicate that the E573EHSLL sequence is an essential component of the endosomal targeting signal in mucolipin-1 cytoplasmic tail.
A di-leucine motif located at C-terminal tail of mucolipin-1 mediates internalization of Tac-MLN-CTail chimera.