LiteFold/DisProt huggingface dataset:
Protein: DP02689 (UniProt Q54BW5)
Region: residues 164	to 179
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Crystallographic analyses of the core enzyme indicated that the C-termini, normally flexible, were constrained by interactions with the shortened N-termini that arose from the loss of residues 1-37.
Homotrimeric structure of D. discoideum dUTPase where the flexible C-terminus of chain A interacts with the N-terminus of chain B and the flexible C-terminus of chain C interacts with the N-terminus of chain A.
Cross-references: PDB:5F9K
Protein: DP02690 (UniProt F4JL28)
Region: residues 195	to 208
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, we failed to obtain crystals of full-length EBS in complex with H3K4me2 or H3K4me3 peptides.
Missing density region in the C-terminal loop (197-234) of the protein
Cross-references: PDB:5Z8L
Protein: DP02690 (UniProt F4JL28)
Region: residues 221	to 234
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
However, we failed to obtain crystals of full-length EBS in complex with H3K4me2 or H3K4me3 peptides.
Missing density region in the C-terminal loop (197-234) of the protein
Cross-references: PDB:5Z8L
Protein: DP02690 (UniProt F4JL28)
Region: residues 200	to 234
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: deletion mutation phenotypic evidence used in manual assertion
Supporting statements:
Notably, EBS adopted an autoinhibition mode to mediate its switch in binding preference between H3K27me3 and H3K4me3.
To investigate the in vivo relevance of the C-terminal autoinhibition loop, we generated a C-terminal deletion mutant and found that it failed to complement the early flowering of ebs (n = 6 independent transgenic lines; Fig. 4a,​,bb and Supplementary Fig. 6d), despite having a much higher protein level than wild-type EBS
Protein: DP02691 (UniProt Q92608)
Region: residues 70	to 80
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The DOCK2 structure is composed of the N-terminal SH3 domain (residues 1–69) and a three-helix bundle domain (residues 81–167; Dα1–3). The electron density of the 11-residue region connecting the two domains was not observed.
Cross-references: PDB:3A98
Protein: DP02691 (UniProt Q92608)
Region: residues 70	to 80
Annotation: flexible linker (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The DOCK2 structure is composed of the N-terminal SH3 domain (residues 1–69) and a three-helix bundle domain (residues 81–167; Dα1–3). The electron density of the 11-residue region connecting the two domains was not observed.
Cross-references: PDB:3A98
Protein: DP02691 (UniProt Q92608)
Region: residues 1621	to 1830
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The polybasic region C-terminal of DOCK2DHR2 (Fig. 1a) is disordered.
Cross-references: EMDB:10498
PDB:6TGC
PDB:6TGB
EMDB:10497
Protein: DP02691 (UniProt Q92608)
Region: residues 70	to 80
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the binary DOCK2-ELMO1 complex and ternary DOCK2-ELMO1-RAC1 complex, show this region lacks electron density indicating it is disordered.
Cross-references: EMDB:10498
PDB:6TGC
PDB:6TGB
EMDB:10497
Protein: DP02691 (UniProt Q92608)
Region: residues 578	to 589
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the binary DOCK2-ELMO1 complex and ternary DOCK2-ELMO1-RAC1 complex, show this region lacks electron density indicating it is disordered.
Cross-references: EMDB:10498
PDB:6TGC
PDB:6TGB
EMDB:10497
Protein: DP02691 (UniProt Q92608)
Region: residues 1257	to 1270
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The electron microscopy evidence of the binary DOCK2-ELMO1 complex and ternary DOCK2-ELMO1-RAC1 complex, show this region lacks electron density indicating it is disordered.
Cross-references: EMDB:10498
PDB:6TGC
PDB:6TGB
EMDB:10497
Protein: DP02692 (UniProt Q6R327)
Region: residues 1	to 191
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
According to the 4.9 Å EM map, we could only build poly-Alanine chains for N-terminal portion of Rictor and five α-helices of mSin1. The rest portions are invisible in the EM map possibly due to their intrinsic flexibility, which is consistent with secondary structure prediction
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02692 (UniProt Q6R327)
Region: residues 1017	to 1610
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
According to the 4.9 Å EM map, we could only build poly-Alanine chains for N-terminal portion of Rictor and five α-helices of mSin1. The rest portions are invisible in the EM map possibly due to their intrinsic flexibility, which is consistent with secondary structure prediction
Rictor has an N-terminal armadillo (ARM) repeat cluster (~900 residues), followed by a large unstructured region
The C-terminal half of Rictor and most of the mSin1 portion are invisible in the EM map, which might result from their intrinsic flexibility.
The C-terminal portion of Rictor could not be assigned in the EM map possibly due to its flexibility.
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02692 (UniProt Q6R327)
Region: residues 1	to 595
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Moreover, mSin1N could bind to the Rictor N-terminal portions containing residues 1–595 or 1–905 and C-terminal portion containing residues 905–1708
Two C-terminal truncations and an N-terminal truncation of Rictor could bind to mTOR
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02692 (UniProt Q6R327)
Region: residues 1	to 905
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Moreover, mSin1N could bind to the Rictor N-terminal portions containing residues 1–595 or 1–905 and C-terminal portion containing residues 905–1708
Two C-terminal truncations and an N-terminal truncation of Rictor could bind to mTOR
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02692 (UniProt Q6R327)
Region: residues 905	to 1708
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Moreover, mSin1N could bind to the Rictor N-terminal portions containing residues 1–595 or 1–905 and C-terminal portion containing residues 905–1708
Two C-terminal truncations and an N-terminal truncation of Rictor could bind to mTOR
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02692 (UniProt Q6R327)
Region: residues 1	to 1708
Annotation: molecular adaptor activity (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The functional core complex consists of mTOR, mLST8, and two mTORC2-specific components, Rictor and mSin1.
Our biochemical and structural analyses demonstrate that Rictor and mSin1 interact with each other and together make multiple contacts with mTOR-mLST8.
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02693 (UniProt Q9BPZ7)
Region: residues 248	to 522
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-terminal half of Rictor and most of the mSin1 portion are invisible in the EM map, which might result from their intrinsic flexibility.
According to the 4.9 Å EM map, we could only build poly-Alanine chains for N-terminal portion of Rictor and five α-helices of mSin1. The rest portions are invisible in the EM map possibly due to their intrinsic flexibility, which is consistent with secondary structure prediction
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02693 (UniProt Q9BPZ7)
Region: residues 1	to 522
Annotation: molecular adaptor activity (Molecular function)
Evidence: cryogenic electron microscopy evidence used in manual assertion
Supporting statements:
The functional core complex consists of mTOR, mLST8, and two mTORC2-specific components, Rictor and mSin1.
mSin1 binds Rictor, MSLT8 and mTOR and is involved in the formation of the complex 
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02693 (UniProt Q9BPZ7)
Region: residues 1	to 522
Annotation: molecular adaptor activity (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
The functional core complex consists of mTOR, mLST8, and two mTORC2-specific components, Rictor and mSin1.
mSin1 binds Rictor, MSLT8 and mTOR and is involved in the formation of the complex 
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02693 (UniProt Q9BPZ7)
Region: residues 1	to 522
Annotation: protein binding (Molecular function)
Evidence: co-immunoprecipitation evidence used in manual assertion
Supporting statements:
Full-length mSin1 bound to the N-terminal portion (residues 1–905) or C-terminal portion (residues 905–1708) of Rictor
The ProA-tagged mSin1 could pull out endogenous mTOR, indicating a direct interaction (Supplementary information, Figure S2b, lanes 1, 3, 4, and 7). Full-length mSin1 and two C-terminal truncations could also pull out the endogenous mTOR in the presence of Rictor
mSin1 bound to mLST8 (lane 4) and the interaction was enhanced when mTOR was overexpressed (lane 6).
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02693 (UniProt Q9BPZ7)
Region: residues 360	to 522
Annotation: molecular function inhibitor activity (Molecular function)
Evidence: combinatorial experimental and author inference evidence contained in single publication used in manual assertion
Supporting statements:
The PH domain of mSin1 inhibits mTORC2 activity and this autoinhibition is released in the presence of phosphatidylinositol (3,4,5)-trisphosphate (PIP3)
Cross-references: EMDB:EMD-6913
PDB:5ZCS
Protein: DP02694 (UniProt Q8WUN7)
Region: residues 1	to 20
Annotation: disorder (Structural state)
Evidence: nuclear magnetic resonance spectroscopy evidence used in manual assertion
Supporting statements:
Moreover, both termini (residues Met1–Ser20 and Pro101–Asn106) are not included in the structural calculation process for their conformational flexibility.
Cross-references: PDB:1TTN
Protein: DP02695 (UniProt Q9JIP3)
Region: residues 396	to 416
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structure is well defined except for a 20 amino acids (A.A.) region connecting strand βC and helix αC (residues 396–416, we named as CC′ segment), the electron density of which is not observable.
Cross-references: PDB:3VBC
Protein: DP02696 (UniProt Q9FLN8)
Region: residues 1	to 24
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The first 49 residues of AtIAMT1 in this particular set of crystal structures form a mobile loop. In fact, recognizable electron density attributable to residues 1 to 24 is noticeably absent from the refined AtIAMT1 crystal structure, which also lacks a bound IAA substrate.
Cross-references: PDB:3B5I
Protein: DP02697 (UniProt Q02363)
Region: residues 1	to 23
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
We have solved the structure of the ID2 homodimer HLH domain (residues 24–82) at a 2.1Å resolution, coupled to a stabilizing 14 amino acid linker region (LKPSFLVQSGDIAS).
Cross-references: PDB:4AYA
Protein: DP02698 (UniProt P54687)
Region: residues 1	to 21
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 hBCATc-ox·4MeVA comprises 358 residues (22-45, 47-193, and 199-385) for subunit 1, 358 residues (24-194 and 199-385) for subunit 2, 2 PLPs, 4MeVAs, and 351 water molecules. The average thermal factor of the main-chain atoms is 24.3 Å2. No interpretable electron density was observed for the residues that are not listed above.
Cross-references: PDB:2COI
PDB:2COJ
PDB:2COG
Protein: DP02699 (UniProt Q6V1X1)
Region: residues 138	to 164
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The DPP8 unliganded form has interpretable electron density from residues 48–70, 77–105, 109–137, and 165–897, while in DPP8 in complex with SLRFLYEG, residues 48–105, 109–139, and 148–897 are well ordered. 
Cross-references: PDB:6EOS
PDB:6EOO
Protein: DP02699 (UniProt Q6V1X1)
Region: residues 148	to 164
Annotation: disorder to order (Structural transition)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The DPP8 unliganded form has interpretable electron density from residues 48–70, 77–105, 109–137, and 165–897, while in DPP8 in complex with SLRFLYEG, residues 48–105, 109–139, and 148–897 are well ordered. 
In intriguing contrast to DPP4, where liganded and unliganded forms are closely similar, ligand binding to DPP8/9 induces an extensive rearrangement at the active site through a disorder-order transition of a 26-residue loop segment, which partially folds into an α-helix (R-helix), including R160/133, a key residue for substrate binding.
Part of this segment folds into the R-helix, which harbors the arginine residues at its C termini. The R-helix becomes ordered upon substrate binding but is mostly disordered in the unliganded forms (Fig. 2 B, D, and E)
Cross-references: PDB:6EOT
PDB:6EOP
Protein: DP02699 (UniProt Q6V1X1)
Region: residues 1	to 47
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The DPP8 unliganded form has interpretable electron density from residues 48–70, 77–105, 109–137, and 165–897, while in DPP8 in complex with SLRFLYEG, residues 48–105, 109–139, and 148–897 are well ordered.
Cross-references: PDB:6EOS
PDB:6EOO
Protein: DP02700 (UniProt P0A8S9)
Region: residues 83	to 116
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-termini of both FlhD monomers (residues 83-116) are completely disrupted by crystal packing, implying that this region of FlhD is highly flexible.
Residues 83–116 in both chains were not interpretable and were not initially modelled.
Protruding from the core are two flexible arms, each composed of ≈ 34 residues of the C‐terminus of each monomer
Thus, our model suggests that the entire C‐terminal sequence (83–116) of each chain is mobile and flexible in the FlhD dimer, so much so that its folding energy is less than the energy necessary to crystallize the protein.
Also, residues 83–116 in chain B and residues 99–116 in chain A are disrupted by crystal packing and cannot be modelled. Thus, this part of the FlhD dimer must be highly flexible in solution and, therefore, its structure should be malleable
Cross-references: PDB:1G8E
Protein: DP02700 (UniProt P0A8S9)
Region: residues 83	to 116
Annotation: flexible C-terminal tail (Disorder function)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The C-termini of both FlhD monomers (residues 83-116) are completely disrupted by crystal packing, implying that this region of FlhD is highly flexible.
Thus, our model suggests that the entire C‐terminal sequence (83–116) of each chain is mobile and flexible in the FlhD dimer, so much so that its folding energy is less than the energy necessary to crystallize the protein.
Thus, the unusually tight packing of protein in this crystal form prevents both C‐termini from adopting a well‐defined structure. The implication is that the C‐terminus is very flexible: sufficiently flexible that the forces involved in crystal packing are greater than the forces folding this region of the FlhD protein.
Cross-references: PDB:1G8E
Protein: DP02701 (UniProt Q15631)
Region: residues 218	to 228
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
In the orthorhombic crystal structure, the first 11 residues, including the His tag  and the spacer sequence before Met1,and the last 11 resides (residues 218-228) are invisible, probably owing to disorder.
The C-terminal segment from residue 218 to the end was poorly defined in each monomer and was not included in the atomic model.
Cross-references: PDB:1J1J
Protein: DP02702 (UniProt Q14995)
Region: residues 386	to 395
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The current atomic model of Rev-erbβ contains residues (396–476) with disordered N and C-terminal tails (residues 386–395 and 477–479).
Cross-references: PDB:2V0V
PDB:2V7C
Protein: DP02702 (UniProt Q14995)
Region: residues 470	to 479
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Careful examination of the structure shows that the region corresponding to the disordered region 470–479 in molecule A exhibits relatively high thermal displacement parameters in all other molecules in both crystal forms, indicating structural mobility of this region
Cross-references: PDB:2V0V
PDB:2V7C
Protein: DP02703 (UniProt O00411)
Region: residues 105	to 217
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
Here we report the X-ray structure of human mtRNAP at 2.5 Å resolution, which reveals a T7-like catalytic carboxy-terminal domain, an amino-terminal domain that remotely resembles the T7 promoter-binding domain, a novel pentatricopeptide repeat domain, and a flexible N-terminal extension.
The refined structure includes residues 218–591, 603–611, 616–735, 770–1085 and 1109–1230.
Cross-references: PDB:3SPA
Protein: DP02703 (UniProt O00411)
Region: residues 592	to 602
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined structure includes residues 218–591, 603–611, 616–735, 770–1085 and 1109–1230.
Disordered region inside the intercalating hairpin
Cross-references: PDB:3SPA
Protein: DP02703 (UniProt O00411)
Region: residues 734	to 769
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined structure includes residues 218–591, 603–611, 616–735, 770–1085 and 1109–1230.
Disordered region inside the "thumb" of the protein
A portion of the thumb (residues 736–769) and the flexible specificity loop (residues 1086–1105) are not visible in the structure, but adjacent elements occupy almost identical positions in T7 RNAP, indicating that these elements have similar orientations and functions.
Cross-references: PDB:3SPA
Protein: DP02703 (UniProt O00411)
Region: residues 1086	to 1108
Annotation: disorder (Structural state)
Evidence: X-ray crystallography-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The refined structure includes residues 218–591, 603–611, 616–735, 770–1085 and 1109–1230.
Disordered region corresponding to the "specificity loop" of the protein
A portion of the thumb (residues 736–769) and the flexible specificity loop (residues 1086–1105) are not visible in the structure, but adjacent elements occupy almost identical positions in T7 RNAP, indicating that these elements have similar orientations and functions.
Cross-references: PDB:3SPA
Protein: DP02703 (UniProt O00411)
Region: residues 39	to 218
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:7PZR
Protein: DP02703 (UniProt O00411)
Region: residues 592	to 602
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:7PZR
Protein: DP02703 (UniProt O00411)
Region: residues 736	to 769
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:7PZR
Protein: DP02703 (UniProt O00411)
Region: residues 1086	to 1108
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
This region lacks electron density, indicating it is disordered.
Cross-references: PDB:7PZR
Protein: DP02704 (UniProt P41214)
Region: residues 184	to 259
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structures, supported by biochemical experiments, reveal how eIF2D emulates the function of several canonical translation initiation factors by using three independent, flexibly connected RNA binding domains to simultaneously monitor codon-anticodon interactions in the ribosomal P-site and position the initiator tRNA.
Cross-references: PDB:5OA3
Protein: DP02704 (UniProt P41214)
Region: residues 348	to 373
Annotation: disorder (Structural state)
Evidence: cryogenic electron microscopy-based structural model with missing residue coordinates used in manual assertion
Supporting statements:
The structures, supported by biochemical experiments, reveal how eIF2D emulates the function of several canonical translation initiation factors by using three independent, flexibly connected RNA binding domains to simultaneously monitor codon-anticodon interactions in the ribosomal P-site and position the initiator tRNA.
Cross-references: PDB:5OA3